HISTORICAL GAAP TO NON-GAAP RECONCILIATION APRIL 21, 2025

2 USE OF NON-GAAP MEASURES This presentation includes financial measures that are not presented in accordance with U.S. generally accepted accounting principles (“Non-GAAP financial measures”). These Non-GAAP financial measures include non-GAAP gross profit, non-GAAP gross margin, non-GAAP operating expenses, non-GAAP operating income, non-GAAP operating margin, non-GAAP income tax provision, Adjusted EBITDA, non-GAAP net income, and non-GAAP diluted earnings per share, and reflect adjustments for the impact of share-based compensation expense and certain items related to restructuring and severance charges and any associated adjustments. Reconciliations of these Non-GAAP financial measures to the most directly comparable financial measures calculated and presented in accordance with GAAP are provided in the financial tables included in this presentation. For further information regarding these Non-GAAP financial measures, please refer to the tables presenting reconciliations of our Non-GAAP results to our GAAP results at the end of this presentation.

3 Summary: Historical GAAP & Non-GAAP Results (in thousands, except per share amounts) For the years ended December 31 2020 2021 2022 2023 2024 Revenue $474,560 $662,428 $919,998 $1,130,604 $1,017,865 Gross Margin 41.8% 43.2% 43.7% 43.5% 44.7% Operating Margin 12.2% 19.2% 23.1% 23.5% 20.7% Net Income $49,982 $98,650 $183,079 $246,263 $200,992 Diluted Earnings Per Share $1.46 $2.88 $5.46 $7.43 $6.15 Non-GAAP Results Non-GAAP Gross Margin 42.0% 43.4% 43.8% 43.6% 44.9% Non-GAAP Operating Margin 14.4% 21.0% 24.5% 25.2% 23.3% Adjusted EBITDA $78,368 $150,112 $237,310 $298,187 $252,991 Non-GAAP Net Income $58,999 $109,027 $194,641 $262,935 $223,768 Non-GAAP Diluted Earnings Per Share $1.73 $3.18 $5.80 $7.93 $6.84

4 Axcelis Technologies Inc. Schedule Reconciling Selected Non-GAAP Financial Measures – Fiscal Year 2020 (in thousands, except per share amounts) Footnotes: 1 Impact of taxes from Non-GAAP adjustments, uses adjusted tax rate of 14% Figures may not sum due to rounding Q1'20 Q2'20 Q3'20 Q4'20 FY 2020 Revenue $ 118,991 $ 122,965 $ 110,405 $ 122,199 $ 474,560 Gross Profit $ 45,549 $ 51,899 $ 48,161 $ 52,975 $ 198,584 Stock-based compensation 147 278 184 213 822 Non-GAAP Gross Profit $ 45,696 $ 52,177 $ 48,345 $ 53,188 $ 199,406 Non-GAAP Gross Margin 38.4% 42.4% 43.8% 43.5% 42.0% Operating Expense $ 31,846 $ 35,518 $ 34,279 $ 38,900 $ 140,543 Stock-based compensation (1,579) (2,805) (2,734) (2,545) (9,663) Non-GAAP Operating Expense $ 30,267 $ 32,713 $ 31,545 $ 36,355 $ 130,880 Operating Income $ 13,703 $ 16,381 $ 13,882 $ 14,075 $ 58,041 Stock-based compensation 1,726 3,083 2,919 2,757 10,485 Non-GAAP Operating Income $ 15,429 $ 19,464 $ 16,801 $ 16,832 $ 68,526 Non-GAAP Operating Margin 13.0% 15.8% 15.2% 13.8% 14.4% Income tax provision $ 1,041 $ 2,271 $ 2,807 $ (215) $ 5,904 Tax impact of non-GAAP adjustments1 242 432 409 386 1,468 Non-GAAP Income tax provision $ 1,283 $ 2,703 $ 3,216 $ 171 $ 7,372 Net Income $ 11,221 $ 13,302 $ 10,785 $ 14,674 $ 49,982 Stock-based compensation 1,726 3,083 2,919 2,757 10,485 Tax impact of non-GAAP adjustments1 (242) (432) (409) (386) (1,468) Non-GAAP Net Income $ 12,705 $ 15,953 $ 13,295 $ 17,045 $ 58,999 Diluted earnings per share $ 0.33 $ 0.39 $ 0.32 $ 0.43 $ 1.46 Stock-based compensation 0.05 0.09 0.09 0.08 0.31 Tax impact of non-GAAP adjustments1 (0.01) (0.01) (0.01) (0.01) (0.04) Non-GAAP diluted earnings per share $ 0.37 $ 0.47 $ 0.39 $ 0.50 $ 1.73 Basic Share O/S 32,872 33,116 33,477 33,548 33,257 Diluted Shares O/S 34,057 33,958 34,174 34,318 34,128 Adjusted EBITDA Reconciliation Q1'20 Q2'20 Q3'20 Q4'20 FY 2020 Net income $ 11,221 $ 13,302 $ 10,785 $ 14,674 $ 49,982 Other (income)/expense 1,440 808 290 (383) 2,156 Income tax provision 1,041 2,271 2,807 (215) 5,904 Depreciation & amortization 2,340 2,440 2,494 2,568 9,842 Subtotal $ 16,043 $ 18,821 $ 16,376 $ 16,644 $ 67,884 Stock-based compensation 1,726 3,083 2,919 2,757 10,485 Adjusted EBITDA $ 17,769 $ 21,904 $ 19,294 $ 19,401 $ 78,368 Adjusted EBITDA Margin 14.9% 17.8% 17.5% 15.9% 16.5%

5 Axcelis Technologies Inc. Schedule Reconciling Selected Non-GAAP Financial Measures – Fiscal Year 2021 (in thousands, except per share amounts) Q1'21 Q2'21 Q3'21 Q4'21 FY 2021 Revenue $ 132,776 $ 147,274 $ 176,694 $ 205,684 $ 662,428 Gross Profit $ 56,435 $ 64,014 $ 76,512 $ 89,484 $ 286,445 Stock-based compensation 279 253 194 229 956 Non-GAAP Gross Profit $ 56,714 $ 64,267 $ 76,706 $ 89,713 $ 287,401 Non-GAAP Gross Margin 42.7% 43.6% 43.4% 43.6% 43.4% Operating Expense $ 36,085 $ 40,017 $ 40,118 $ 42,900 $ 159,120 Stock-based compensation (2,127) (3,125) (2,990) (2,869) (11,111) Non-GAAP Operating Expense $ 33,958 $ 36,892 $ 37,128 $ 40,031 $ 148,009 Operating Income $ 20,350 $ 23,997 $ 36,394 $ 46,584 $ 127,325 Stock-based compensation 2,406 3,378 3,185 3,098 12,067 Non-GAAP Operating Income $ 22,756 $ 27,375 $ 39,579 $ 49,682 $ 139,392 Non-GAAP Operating Margin 17.1% 18.6% 22.4% 24.2% 21.0% Income tax provision $ 1,721 $ 3,843 $ 6,698 $ 9,517 $ 21,778 Tax impact of non-GAAP adjustments1 337 473 446 434 1,689 Non-GAAP Income tax provision $ 2,057 $ 4,316 $ 7,144 $ 9,951 $ 23,468 Net Income $ 16,480 $ 18,906 $ 27,515 $ 35,749 $ 98,650 Stock-based compensation 2,406 3,378 3,185 3,098 12,067 Tax impact of non-GAAP adjustments1 (337) (473) (446) (434) (1,689) Non-GAAP Net Income $ 18,549 $ 21,811 $ 30,254 $ 38,413 $ 109,027 Diluted earnings per share $ 0.48 $ 0.55 $ 0.81 $ 1.05 $ 2.88 Stock-based compensation 0.07 0.10 0.09 0.09 0.35 Tax impact of non-GAAP adjustments1 (0.01) (0.01) (0.01) (0.01) (0.05) Non-GAAP diluted earnings per share $ 0.54 $ 0.64 $ 0.89 $ 1.13 $ 3.18 Basic Share O/S 33,715 33,677 33,537 33,295 33,555 Diluted Shares O/S 34,643 34,311 34,089 34,011 34,268 Adjusted EBITDA Reconciliation Q1'21 Q2'21 Q3'21 Q4'21 FY 2021 Net income $ 16,480 $ 18,906 $ 27,515 $ 35,749 $ 98,650 Other (income)/expense 2,149 1,250 2,180 1,318 6,896 Income tax provision 1,721 3,843 6,698 9,517 21,778 Depreciation & amortization 2,621 2,667 2,632 2,801 10,721 Subtotal $ 22,970 $ 26,665 $ 39,025 $ 49,386 $ 138,045 Stock-based compensation 2,406 3,378 3,185 3,098 12,067 Adjusted EBITDA $ 25,376 $ 30,043 $ 42,210 $ 52,484 $ 150,112 Adjusted EBITDA Margin 19.1% 20.4% 23.9% 25.5% 22.7% Footnotes: 1 Impact of taxes from Non-GAAP adjustments, uses adjusted tax rate of 14% Figures may not sum due to rounding

6 Axcelis Technologies Inc. Schedule Reconciling Selected Non-GAAP Financial Measures – Fiscal Year 2022 (in thousands, except per share amounts) Q1'22 Q2'22 Q3'22 Q4'22 FY 2022 Revenue $ 203,595 $ 221,177 $ 229,175 $ 266,051 $ 919,998 Gross Profit $ 89,766 $ 99,181 $ 103,321 $ 109,521 $ 401,790 Stock-based compensation 207 318 225 269 1,019 Non-GAAP Gross Profit $ 89,973 $ 99,499 $ 103,546 $ 109,790 $ 402,809 Non-GAAP Gross Margin 44.2% 45.0% 45.2% 41.3% 43.8% Operating Expense $ 40,843 $ 45,035 $ 50,119 $ 53,432 $ 189,429 Stock-based compensation (2,493) (3,208) (3,337) (3,386) (12,425) Non-GAAP Operating Expense $ 38,350 $ 41,827 $ 46,782 $ 50,046 $ 177,004 Operating Income $ 48,923 $ 54,145 $ 53,202 $ 56,089 $ 212,361 Stock-based compensation 2,701 3,526 3,562 3,655 13,444 Non-GAAP Operating Income $ 51,624 $ 57,671 $ 56,764 $ 59,744 $ 225,805 Non-GAAP Operating Margin 25.4% 26.1% 24.8% 22.5% 24.5% Income tax provision $ 4,269 $ 4,007 $ 4,726 $ 8,804 $ 21,806 Tax impact of non-GAAP adjustmets1 378 494 499 512 1,882 Non-GAAP Income tax provision $ 4,647 $ 4,501 $ 5,225 $ 9,316 $ 23,688 Net Income $ 41,614 $ 44,189 $ 40,283 $ 56,992 $ 183,079 Stock-based compensation 2,701 3,526 3,562 3,655 13,444 Tax impact of non-GAAP adjustments1 (378) (494) (499) (512) (1,882) Non-GAAP Net Income $ 43,937 $ 47,221 $ 43,347 $ 60,136 $ 194,641 Diluted earnings per share $ 1.22 $ 1.32 $ 1.21 $ 1.71 $ 5.46 Stock-based compensation 0.08 0.11 0.11 0.11 0.40 Tax impact of non-GAAP adjustments1 (0.01) (0.01) (0.01) (0.02) (0.06) Non-GAAP diluted earnings per share $ 1.29 $ 1.41 $ 1.30 $ 1.81 $ 5.80 Basic Share O/S 33,245 33,096 33,011 32,823 33,043 Diluted Shares O/S 33,974 33,562 33,389 33,262 33,542 Adjusted EBITDA Reconciliation Q1'22 Q2'22 Q3'22 Q4'22 FY 2022 Net income $ 41,614 $ 44,189 $ 40,283 $ 56,992 $ 183,079 Other (income)/expense 3,040 5,949 8,193 (9,707) 7,475 Income tax provision 4,269 4,007 4,726 8,804 21,806 Depreciation & amortization 2,824 2,851 2,866 2,965 11,506 Subtotal $ 51,747 $ 56,996 $ 56,068 $ 59,054 $ 223,865 Stock-based compensation 2,701 3,526 3,562 3,655 13,444 Adjusted EBITDA $ 54,448 $ 60,522 $ 59,630 $ 62,710 $ 237,310 Adjusted EBITDA Margin 26.7% 27.4% 26.0% 23.6% 25.8% Footnotes: 1 Impact of taxes from Non-GAAP adjustments, uses adjusted tax rate of 14% Figures may not sum due to rounding

7 Axcelis Technologies Inc. Schedule Reconciling Selected Non-GAAP Financial Measures – Fiscal Year 2023 (in thousands, except per share amounts) Footnotes: 1 Impact of taxes from Non-GAAP adjustments, uses adjusted tax rate of 14% Figures may not sum due to rounding Q1'23 Q2'23 Q3'23 Q4'23 FY 2023 Revenue $ 254,020 $ 273,970 $ 292,326 $ 310,288 $ 1,130,604 Gross Profit $ 104,019 $ 119,703 $ 129,684 $ 137,896 $ 491,301 Stock-based compensation 215 396 308 337 1,255 Non-GAAP Gross Profit $ 104,233 $ 120,099 $ 129,992 $ 138,233 $ 492,556 Non-GAAP Gross Margin 41.0% 43.8% 44.5% 44.5% 43.6% Operating Expense $ 52,662 $ 55,995 $ 58,004 $ 58,845 $ 225,506 Bad debt expense - - (653) (464) (1,117) Stock-based compensation (2,989) (4,348) (4,773) (4,904) (17,014) Non-GAAP Operating Expense $ 49,673 $ 51,647 $ 52,577 $ 53,478 $ 207,375 Operating Income $ 51,357 $ 63,708 $ 71,680 $ 79,051 $ 265,795 Bad debt expense - - 653 464 1,117 Stock-based compensation 3,203 4,744 5,081 5,240 18,269 Non-GAAP Operating Income $ 54,560 $ 68,452 $ 77,415 $ 84,755 $ 285,181 Non-GAAP Operating Margin 21.5% 25.0% 26.5% 27.3% 25.2% Income tax provision $ 5,205 $ 3,037 $ 7,744 $ 16,350 $ 32,336 Tax impact of non-GAAP adjustments1 448 664 803 799 2,714 Non-GAAP Income tax provision $ 5,653 $ 3,701 $ 8,547 $ 17,149 $ 35,050 Net Income $ 47,697 $ 61,579 $ 65,931 $ 71,056 $ 246,263 Bad debt expense - - 653 464 1,117 Stock-based compensation 3,203 4,744 5,081 5,240 18,269 Tax impact of non-GAAP adjustments1 (448) (664) (803) (799) (2,714) Non-GAAP Net Income $ 50,452 $ 65,659 $ 70,863 $ 75,961 $ 262,935 Diluted earnings per share $ 1.43 $ 1.86 $ 1.99 $ 2.15 $ 7.43 Bad debt expense - - 0.02 0.01 0.03 Stock-based compensation 0.10 0.14 0.15 0.16 0.55 Tax impact of non-GAAP adjustments1 (0.01) (0.02) (0.02) (0.02) (0.08) Non-GAAP diluted earnings per share $ 1.52 $ 1.98 $ 2.14 $ 2.30 $ 7.93 Basic Share O/S 32,744 32,775 32,807 32,708 32,758 Diluted Shares O/S 33,293 33,189 33,159 33,031 33,165 Adjusted EBITDA Reconciliation Q1'23 Q2'23 Q3'23 Q4'23 FY 2023 Net income $ 47,697 $ 61,579 $ 65,931 $ 71,056 $ 246,263 Other (income)/expense (1,545) (908) (1,995) (8,355) (12,803) Income tax provision 5,205 3,037 7,744 16,350 32,336 Depreciation & amortization 3,077 3,164 3,211 3,552 13,004 Subtotal $ 54,434 $ 66,872 $ 74,891 $ 82,603 $ 278,800 Bad debt expense - - 653 464 1,117 Stock-based compensation 3,203 4,744 5,081 5,240 18,269 Adjusted EBITDA $ 57,637 $ 71,616 $ 80,626 $ 88,307 $ 298,187 Adjusted EBITDA Margin 22.7% 26.1% 27.6% 28.5% 26.4%

8 Axcelis Technologies Inc. Schedule Reconciling Selected Non-GAAP Financial Measures – Fiscal Year 2024 (in thousands, except per share amounts) Footnotes: 1Restructuring and other costs primarily related to early retirement programs and severance costs, due to global cost-saving initiatives 2 Impact of taxes from Non-GAAP adjustments, uses adjusted tax rate of 14% Figures may not sum due to rounding Q1'24 Q2'24 Q3'24 Q4'24 FY 2024 Revenue $ 252,372 $ 256,512 $ 256,564 $ 252,417 $ 1,017,865 Gross Profit $ 116,051 $ 112,409 $ 109,970 $ 116,223 $ 454,654 Restructuring1 - 876 - 256 1,133 Stock-based compensation 290 462 354 399 1,505 Non-GAAP Gross Profit $ 116,341 $ 113,747 $ 110,324 $ 116,879 $ 457,291 Non-GAAP Gross Margin 46.1% 44.3% 43.0% 46.3% 44.9% Operating Expense $ 59,512 $ 59,599 $ 63,057 $ 61,692 $ 243,860 Bad debt expense 458 - (3,445) - (2,986) Restructuring1 - (552) - (862) (1,414) Stock-based compensation (4,401) (5,008) (5,057) (4,980) (19,446) Non-GAAP Operating Expense $ 55,570 $ 54,039 $ 54,555 $ 55,850 $ 220,014 Operating Income $ 56,539 $ 52,810 $ 46,913 $ 54,531 $ 210,794 Bad debt expense (458) - 3,445 - 2,986 Restructuring1 - 1,429 - 1,118 2,547 Stock-based compensation 4,690 5,469 5,411 5,380 20,951 Non-GAAP Operating Income $ 60,771 $ 59,708 $ 55,769 $ 61,029 $ 237,278 Non-GAAP Operating Margin 24.1% 23.3% 21.7% 24.2% 23.3% Income tax provision $ 7,404 $ 6,399 $ 6,789 $ 8,689 $ 29,282 Tax impact of non-GAAP adjustments2 593 966 1,240 910 3,708 Non-GAAP Income tax provision $ 7,997 $ 7,365 $ 8,029 $ 9,599 $ 32,990 Net Income $ 51,595 $ 50,866 $ 48,576 $ 49,956 $ 200,992 Bad debt expense (458) - 3,445 - 2,986 Restructuring1 - 1,429 - 1,118 2,547 Stock-based compensation 4,690 5,469 5,411 5,380 20,951 Tax impact of non-GAAP adjustments2 (593) (966) (1,240) (910) (3,708) Non-GAAP Net Income $ 55,234 $ 56,798 $ 56,192 $ 55,544 $ 223,768 Diluted earnings per share $ 1.57 $ 1.55 $ 1.49 $ 1.54 $ 6.15 Bad debt expense (0.01) - 0.11 - 0.09 Restructuring1 - 0.04 - 0.03 0.08 Stock-based compensation 0.14 0.17 0.17 0.17 0.64 Tax impact of non-GAAP adjustments2 (0.02) (0.03) (0.04) (0.03) (0.11) Non-GAAP diluted earnings per share $ 1.68 $ 1.73 $ 1.72 $ 1.71 $ 6.84 Basic Share O/S 32,638 32,598 32,550 32,424 32,552 Diluted Shares O/S 32,926 32,771 32,675 32,514 32,704 Adjusted EBITDA Reconciliation Q1'24 Q2'24 Q3'24 Q4'24 FY 2024 Net income $ 51,595 $ 50,866 $ 48,576 $ 49,956 $ 200,992 Other (income)/expense (2,460) (4,455) (8,452) (4,114) (19,480) Income tax provision 7,404 6,399 6,789 8,689 29,282 Depreciation & amortization 3,750 3,837 3,877 4,250 15,713 Subtotal $ 60,289 $ 56,646 $ 50,790 $ 58,781 $ 226,506 Bad debt expense (458) - 3,445 - 2,986 Restructuring1 - 1,429 - 1,118 2,547 Stock-based compensation 4,690 5,469 5,411 5,380 20,951 Adjusted EBITDA $ 64,521 $ 63,545 $ 59,646 $ 65,279 $ 252,991 Adjusted EBITDA Margin 25.6% 24.8% 23.2% 25.9% 24.9%