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| Career Homeruns Allowed Leaderboard | |
| * - Indicates Hall of Fame Bold - Indicates active player |
| Rank | Player | Homeruns Allowed | IP | Years | Single Season Leaderboard |
| 1. | Skip Burns | 529 | 4027.6 | 2001-2020 | |
| 2. | David Echegaray | 516 | 4812.6 | 2003-2026 | |
| 3. | Jose Langlois | 474 | 3377.9 | 2004-2020 | |
| 4. | Gregory Hart | 441 | 2858.3 | 2000-2012 | |
| 5. | Ryan Turner * | 373 | 3744.9 | 2001-2021 | |
| 6. | J.J. Cobb | 371 | 3210.6 | 2000-2014 | |
| 7. | Mark Torrence | 364 | 2896.3 | 2002-2015 | |
| 8. | Steven Williams * | 360 | 3524.0 | 2002-2017 | |
| Richard Hirsh | 360 | 3209.9 | 2000-2012 | ||
| 10. | Mark Trowers | 351 | 3535.9 | 2010-2025 | |
| 11. | Xavier Josephs | 339 | 2994.6 | 2003-2018 | |
| Jeeves Vanhooten | 339 | 3186.9 | 2000-2014 | ||
| 13. | Paul Wendler | 333 | 2332.6 | 2002-2015 | |
| Thomas Maurer | 333 | 2171.9 | 2001-2012 | ||
| 15. | Hugh Hoots | 331 | 3766.6 | 2002-2018 | |
| 16. | Donte Dasilva | 325 | 3018.0 | 2003-2017 | |
| 17. | James Alexander | 319 | 2806.6 | 2011-2026 | |
| 18. | Gene Foxworth | 315 | 2256.6 | 2001-2012 | |
| 19. | Armand Banuelos | 312 | 3088.0 | 2000-2012 | |
| 20. | Ridge Thompson | 308 | 2447.6 | 2006-2020 | |
| 21. | Randy Kennedy | 306 | 2598.6 | 2000-2010 | |
| 22. | Dennis Wright * | 301 | 3380.6 | 2001-2014 | |
| 23. | Aaron Bacon * | 300 | 3356.0 | 2000-2012 | |
| 24. | Lucas Lara | 299 | 2535.0 | 2004-2017 | |
| 25. | James Yim * | 295 | 4445.9 | 2003-2021 | |
| 26. | Matthew Bedard | 293 | 2565.3 | 2004-2015 | |
| 27. | Dirk Carr | 290 | 2559.3 | 2007-2019 | |
| 28. | Paul Knutson | 289 | 2506.3 | 2005-2018 | |
| 29. | Abraham Grayston | 286 | 3311.3 | 2006-2022 | |
| 30. | William Bennington | 285 | 2129.6 | 2003-2014 | |
| 31. | Artur Sax | 284 | 2590.6 | 2013-2025 | |
| 32. | Joe O'Malley | 283 | 2718.6 | 2003-2016 | |
| Thomas Showers * | 283 | 3348.0 | 2000-2013 | ||
| Michael Davis | 283 | 1958.0 | 2004-2013 | ||
| 35. | Galon Thrace | 281 | 2419.3 | 2014-2024 | |
| 36. | Jeffrey Cargo | 279 | 2881.3 | 2000-2011 | |
| 37. | Russ Gobbler | 278 | 2781.6 | 2016-2029 | |
| 38. | Alex Ramirez | 276 | 2007.9 | 2001-2015 | |
| 39. | Albert Olmos | 269 | 3489.6 | 2000-2014 | |
| 40. | Damien Holcombe | 268 | 2356.6 | 2008-2019 | |
| 41. | Glen Robinson | 264 | 2060.6 | 2004-2018 | |
| Malik Meng | 264 | 2438.6 | 2000-2009 | ||
| 43. | Roger Morrison | 263 | 2573.6 | 2002-2013 | |
| 44. | Geoff Stagner | 262 | 2609.0 | 2011-2025 | |
| 45. | Christopher Millar | 261 | 2633.3 | 2014-2029 | |
| 46. | Bobby Williams | 259 | 2170.3 | 2019-2029 | |
| 47. | Leon Collins | 256 | 2526.3 | 2015-2027 | |
| 48. | Ringo Russmyer | 255 | 2224.0 | 2007-2018 | |
| 49. | Rafael Souza | 249 | 2287.6 | 2003-2022 | |
| 50. | Anthony McCulloch | 248 | 1990.6 | 2002-2010 | |
| 51. | Robert Seaborn | 245 | 2156.3 | 2002-2014 | |
| 52. | Edgardo Castillo * | 243 | 3758.6 | 2001-2018 | |
| Luis Marrufo | 243 | 1848.3 | 2002-2012 | ||
| 54. | Eliseo Cordova | 242 | 1668.9 | 2007-2018 | |
| 55. | Russell Hults | 241 | 2887.3 | 2005-2020 | |
| 56. | Alfred Marenco | 239 | 2677.0 | 2005-2016 | |
| 57. | Fred Washington | 237 | 2303.3 | 2005-2019 | |
| 58. | Max Guerra | 235 | 2120.3 | 2008-2020 | |
| 59. | Higinio Delmonte | 234 | 3025.3 | 2014-2029 | |
| 60. | Chad Schmidt | 233 | 3346.6 | 2015-2029 | |
| Charles Lewandowski | 233 | 2454.3 | 2017-2029 | ||
| 62. | Aaron Hightower | 231 | 2198.6 | 2015-2029 | |
| Scott Dutton | 231 | 2324.9 | 2011-2025 | ||
| 64. | Scott Bartell | 229 | 4101.3 | 2003-2021 | |
| 65. | Dennis Morelock * | 228 | 4013.6 | 2003-2017 | |
| 66. | Gilbert Giglio | 227 | 2069.3 | 2014-2029 | |
| Adrian Pantas | 227 | 1981.3 | 2013-2024 | ||
| Randall Spates | 227 | 2129.3 | 2006-2018 | ||
| 69. | Joseph Clark | 222 | 1745.0 | 2014-2028 | |
| 70. | Bruce Sikes | 221 | 2269.0 | 2017-2029 | |
| Roberto Villagomez | 221 | 2099.3 | 2013-2024 | ||
| Emeril Loux | 221 | 2540.0 | 2004-2018 | ||
| 73. | Kelly Giuliani | 220 | 1553.0 | 2000-2007 | |
| 74. | Joseph Bingman | 215 | 2104.3 | 2003-2014 | |
| 75. | Toney Morales | 214 | 2297.6 | 2006-2019 | |
| Ramon Quintana | 214 | 2180.3 | 2000-2013 | ||
| 77. | Joseph Smartt | 213 | 2503.3 | 2002-2014 | |
| 78. | Powell Hoffman | 212 | 2091.7 | 2020-2029 | |
| 79. | Osvaldo Pedraza | 211 | 3311.0 | 2003-2017 | |
| Richard Thornton | 211 | 1866.0 | 2004-2013 | ||
| 81. | Emerson East | 209 | 1703.6 | 2009-2022 | |
| 82. | Derek Host | 208 | 2628.0 | 2012-2026 | |
| 83. | Chet McKie | 207 | 2146.0 | 2013-2023 | |
| 84. | Humberto Deleon | 205 | 3174.9 | 2014-2029 | |
| 85. | Charlie Hester | 204 | 2308.3 | 2017-2028 | |
| John Munson | 204 | 2152.3 | 2016-2026 | ||
| 87. | Curtis Yoo | 202 | 2331.9 | 2013-2027 | |
| Benjamin Alcala | 202 | 2609.6 | 2000-2014 | ||
| Alfonso Arevalo | 202 | 2110.6 | 2000-2011 | ||
| 90. | Peter Iuvani | 201 | 1776.0 | 2011-2021 | |
| 91. | Silverio Osuna | 200 | 1860.6 | 2020-2029 | |
| Ivan Banabila | 200 | 1418.3 | 2008-2026 | ||
| Fred McFinn | 200 | 2353.6 | 2013-2025 | ||
| Michael Hesson | 200 | 1494.0 | 2000-2010 | ||
| 95. | Tobias Escobar | 198 | 2817.9 | 2006-2019 | |
| Charlie Clowers | 198 | 2168.3 | 2008-2019 | ||
| Dustin Carrasquillo | 198 | 2135.3 | 2000-2010 | ||
| 98. | Dan Entrekin | 197 | 1950.3 | 2000-2009 | |
| 99. | Paul Hall | 196 | 2664.0 | 2018-2029 | |
| Robert Silvera | 196 | 2350.0 | 2015-2028 |
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