| 1 | 9:06.01 | Tim McGowanNorthport | Northport '14 | New York State Track & Field Championships | 2014 |
| 2 | 9:06.85 | Kyle MerberHalf Hollow Hills West | Half Hollow Hills West '08 | Boys Division Championship Meet | 2008 |
| 3 | 9:09.65 | Ryan UdvadiaShoreham-Wading River | Shoreham-Wading River '14 | New York State Track & Field Championships | 2014 |
| 4 | 9:10.41 | James JoyWard Melville | Ward Melville '06 | Boys SQ Results 2B | 2006 |
| 5 | 9:12.25 | Bobby AndrewsShoreham-Wading River | Shoreham-Wading River '09 | Section XI Individual Championships | 2009 |
| 6 | 9:12.28 | Mike BranniganNorthport | Northport '15 | Boys Division Championship Meet | 2014 |
| 7 | 9:13.52 | Ryan KutchSt. Anthony's | St. Anthony's '16 | Saint Anthony's Invitational | 2016 |
| 8 | 9:14.25 | Kris MoranNorth Babylon | North Babylon '13 | Boys Division Championship Meet | 2012 |
| 9 | 9:14.56 | Kevin TschirhartNorthport | Northport '05 | Section XI Individual Championships | 2004 |
| 10 | 9:14.87 | Patrick TuckerSt. Anthony's | St. Anthony's '15 | New York State Track & Field Championships | 2014 |
| 11 | 9:15.42 | Robert KrauseConnetquot | Connetquot '06 | Boys SQ Results 2B | 2006 |
| 12 | 9:15.51 | Jack McGowanNorthport | Northport '14 | Boys Division Championship Meet | 2014 |
| 13 | 9:16.40 | Domenick DeMatteoHalf Hollow Hills West | Half Hollow Hills West '09 | Section XI Individual Championships | 2009 |
| 14 | 9:17.85 | Kyle FiasconaroCommack | Commack '04 | Section XI Individual Championships | 2004 |
| 15 | 9:17.94 | Jack MorelliSt. Anthony's | St. Anthony's '24 | St. Anthony's Invitational | 2024 |
| 16 | 9:18.82 | Quinn RasemanWard Melville | Ward Melville '10 | Section XI Individual Championships | 2010 |
| 17 | 9:20.64 | Anthony AnatolWard Melville | Ward Melville '26 | Section XI State Qualifer Day 1 | 2026 |
| 18 | 9:20.72 | Andrew SenfWard Melville | Ward Melville '27 | Section XI State Qualifer Day 1 | 2026 |
| 19 | 9:20.92 | Mason GatewoodSt. Anthony's | St. Anthony's '18 | 47th Saint Anthony's Invitational | 2018 |
| 20 | 9:20.93 | Zach KrauseConnetquot | Connetquot '11 | Section XI Individual Championships | 2010 |
| 21 | 9:21.02 | Michael DamatoWalt Whitman | Walt Whitman '13 | Boys Division Championship Meet | 2012 |
| 22 | 9:21.09 | Jake AlbertLindenhurst | Lindenhurst '25 | Suffolk 1A County Championships | 2025 |
| 23 | 9:21.14 | Seamus TaylorNorthport | Northport '27 | Section XI State Qualifer Day 1 | 2026 |
| 24 | 9:21.32 | Ryan ScanlonHarborfields | Harborfields '16 | Saint Anthony's Invitational | 2016 |
| 25 | 9:21.41 | Ryan SheridanWalt Whitman | Walt Whitman '07 | Section XI Individual Championships | 2004 |
| 26 | 9:21.64 | Evan BloombergNorthport | Northport '09 | Section XI Individual Championships | 2009 |
| 27 | 9:22.50 | Ryan ColabellaHauppauge | Hauppauge '12 | Boys Division Championship Meet | 2012 |
| 28 | 9:22.79 | Vincent CicaleWard Melville | Ward Melville '13 | Boys Division Championship Meet | 2013 |
| 29 | 9:23.23 | Craig NelsonWest Islip | West Islip '14 | Section XI Individual Championships | 2014 |
| 30 | 9:23.34 | Alex SaavedraSachem East | Sachem East '11 | Section XI Individual Championships | 2011 |
| 31 | 9:24.06 | Giovanni SignorettiSmithtown West | Smithtown West '08 | Section XI Individual Championships | 2008 |
| 32 | 9:24.12 | John LeeShoreham-Wading River | Shoreham-Wading River '12 | Saint Anthony's Invitational | 2012 |
| 33 | 9:24.31 | Frank FezzaSachem North | Sachem North '09 | Boys Division Championship Meet | 2009 |
| 34 | 9:24.57 | Zachary CammerWalt Whitman | Walt Whitman '13 | Boys Division Championship Meet | 2012 |
| 35 | 9:24.61 | Ben TuttleEastport-South Manor | Eastport-South Manor '11 | Saint Anthony's Invitational | 2011 |
| 36 | 9:24.68 | Barry FranklinLongwood | Longwood '08 | Section XI Individual Championships | 2008 |
| 37 | 9:24.82 | Joshua HadityCommack | Commack '15 | Boys Division Championship Meet | 2015 |
| 38 | 9:24.95 | Isaac Garcia-CassaniSachem North | Sachem North '14 | Boys Division Championship Meet | 2014 |
| 39 | 9:25.83 | Chad MaierWalt Whitman | Walt Whitman '15 | Saint Anthony's Invitational | 2015 |
| 40 | 9:26.26 | Alex FitzgeraldWard Melville | Ward Melville '13 | Boys Division Championship Meet | 2012 |
| 41 | 9:26.28 | Hartley SemmesHarborfields | Harborfields '25 | St. Anthony's Invitational | 2024 |
| 42 | 9:26.57 | James VallarWalt Whitman | Walt Whitman '13 | Boys Division Championship Meet | 2012 |
| 43 | 9:26.95 | Douglas AntakySmithtown West | Smithtown West '24 | Bob Pratt Invitational | 2024 |
| 44 | 9:27.11 | Connor CrowleyBayport-Blue Point | Bayport-Blue Point '11 | Section XI Individual Championships | 2011 |
| 45 | 9:27.31 | Nicholas CipollaSmithtown West | Smithtown West '18 | Section XI State Qualifier Championships | 2018 |
| 46 | 9:27.33 | Geary GubbinsSouthampton | Southampton '05 | Saint Anthony's Invitational | 2004 |
| 47 | 9:27.50 | Andre SilvaCentereach | Centereach '04 | Suffolk County Boys | 2004 |
| 48 | 9:28.12 | Dylan ConwayHauppauge | Hauppauge '08 | Section XI Individual Championships | 2008 |
| 49 | 9:28.37 | Brendan MartinSmithtown West | Smithtown West '07 | Boys Division Championships 07b | |
| 50 | 9:28.49 | Colin AndersonNorthport | Northport '09 | Section XI Individual Championships | 2008 |
| 51 | 9:28.63 | Jonathan LauerSachem North | Sachem North '17 | Boys Division Championship Meet | 2015 |
| 52 | 9:28.96 | Sam ByrdCommack | Commack '24 | St. Anthony's Invitational | 2024 |
| 53 | 9:29.15 | Joseph BelfordBay Shore | Bay Shore '25 | Suffolk 1A County Championships | 2025 |
| 54 | 9:29.77 | Christopher LangerSt. Anthony's | St. Anthony's '16 | Saint Anthony's Invitational | 2015 |
| 55 | 9:30.06 | Joseph TuckerSt. Anthony's | St. Anthony's '15 | NSCHSAA League Championships | 2015 |
| 56 | 9:30.25 | Austin ConeysHarborfields | Harborfields '12 | Smithtown Invitational | 2011 |
| 57 | 9:30.30 | Douglas ReadSayville | Sayville '18 | North Shore Invitational | 2018 |
| 58 | 9:30.47 | Mike GibneyShoreham-Wading River | Shoreham-Wading River '04 | Suffolk County Boys | 2004 |
| 59 | 9:31.31 | Greg CantwellWard Melville | Ward Melville '05 | Boys Division Championship Meet | 2005 |
| 60 | 9:31.39 | Matthew FlynnSt. Anthony's | St. Anthony's '04 | Saint Anthony's Invitational | 2004 |
| 61 | 9:31.42 | Patrick GintySmithtown East | Smithtown East '13 | Saint Anthony's Invitational | 2012 |
| 62 | 9:31.86 | Brandon SalazarBrentwood | Brentwood '27 | Section XI State Qualifer Day 1 | 2026 |
| 63 | 9:31.97 | Sean GrossmanHalf Hollow Hills East | Half Hollow Hills East '14 | Boys Division Championship Meet | 2014 |
| 64 | 9:32.31 | Timothy KeeganSt. Anthony's | St. Anthony's '07 | Saint Anthony’s Invitational | |
| 65 | 9:32.47 | Will KearnsWesthampton Beach | Westhampton Beach '08 | Section XI Individual Championships | 2008 |
| 66 | 9:32.47 | Brandon CamenzuliSt. John the Baptist | St. John the Baptist '11 | Saint Anthony's Invitational | 2011 |
| 67 | 9:32.53 | Cameron ConeysHarborfields | Harborfields '12 | Smithtown Invitational | 2012 |
| 68 | 9:33.36 | Michael CatalanoSmithtown West | Smithtown West '12 | Boys Division Championship Meet | 2012 |
| 69 | 9:33.53 | Tyler MurthaConnetquot | Connetquot '11 | Saint Anthony's Invitational | 2011 |
| 70 | 9:34.22 | Kal LewisShelter Island | Shelter Island '20 | Westhampton Beach Invitational | 2018 |
| 71 | 9:34.40 | Anthony CocciaSachem North | Sachem North '14 | Westhampton Beach Invitational | 2014 |
| 72 | 9:34.74 | Dan O'ConnorNorthport | Northport '18 | Section XI Boys Division Championships | 2018 |
| 73 | 9:35.17 | Ryan MedinaSachem North | Sachem North '25 | Suffolk 1A County Championships | 2025 |
| 74 | 9:35.44 | Edward LessingSt. Anthony's | St. Anthony's '27 | NSCHSAA Championships | 2025 |
| 75 | 9:35.50 | Isaiah ClaiborneNorthport | Northport '18 | Section XI Boys Division Championships | 2018 |
| 76 | 9:35.54 | Elijah ClaiborneNorthport | Northport '18 | Section XI Boys Division Championships | 2018 |
| 77 | 9:35.67 | Amani MorrellSt. Anthony's | St. Anthony's '18 | Eastern States Invitational | 2017 |
| 78 | 9:35.81 | John OnkenSachem North | Sachem North '15 | Westhampton Beach Invitational | 2015 |
| 79 | 9:35.82 | Lloyd WebbWard Melville | Ward Melville '13 | Boys Division Championship Meet | 2013 |
| 80 | 9:35.84 | Sean RyanNorthport | Northport '19 | Section XI Boys Division Championships | 2018 |
| 81 | 9:35.92 | Eric ZulkofskeWard Melville | Ward Melville '18 | Section XI Boys Division Championships | 2018 |
| 82 | 9:36.25 | Carlos SantosPatchogue-Medford | Patchogue-Medford '18 | Section XI Boys Division Championships | 2018 |
| 83 | 9:36.55 | Matthew TaddeoSt. Anthony's | St. Anthony's '13 | Smithtown Invitational | 2012 |
| 84 | 9:36.55 | Thomas FodorNorthport | Northport '20 | Section XI Boys Division Championships | 2018 |
| 85 | 9:36.58 | Jason SantosSmithtown West | Smithtown West '09 | Boys Division Championship Meet | 2009 |
| 86 | 9:36.95 | Jeremy MiekleyMiller Place | Miller Place '14 | Westhampton Beach Invitational | 2014 |
| 87 | 9:37.08 | Dylan ManningCommack | Commack '25 | St. Anthony's Invitational | 2024 |
| 88 | 9:37.20 | Sawyer BrummNorthport | Northport '29 | Section XI State Qualifer Day 1 | 2026 |
| 89 | 9:37.37 | Alex KramerNorthport | Northport '13 | Boys Division Championship Meet | 2013 |
| 90 | 9:37.95 | Shamar PowellWalt Whitman | Walt Whitman '15 | Bob Pratt Memorial Track & Field Invitational | 2015 |
| 91 | 9:38.01 | Benjamin WindischWalt Whitman | Walt Whitman '10 | Section XI Individual Championships | 2010 |
| 92 | 9:38.20 | James EsernioWard Melville | Ward Melville '15 | Saint Anthony's Invitational | 2015 |
| 93 | 9:38.29 | Chaz AbadWard Melville | Ward Melville '11 | Section XI Individual Championships | 2011 |
| 94 | 9:38.32 | Donato GeraciLongwood | Longwood '11 | Boys Division Championship Meet | 2010 |
| 95 | 9:38.44 | Brendan ZengCommack | Commack '18 | Section XI Boys Division Championships | 2018 |
| 96 | 9:38.70 | Christopher JonesRiverhead | Riverhead '25 | Suffolk 1A County Championships | 2025 |
| 97 | 9:38.88 | James DickinsonNorthport | Northport '13 | Boys Division Championship Meet | 2012 |
| 98 | 9:39.02 | Brendan ConnellSmithtown East | Smithtown East '09 | Boys Division Championships 07b | |
| 99 | 9:39.21 | Todd SatherSt. Anthony's | St. Anthony's '09 | NSCHSAA League Championships | 2009 |
| 100 | 9:39.27 | James BurkePort Jefferson | Port Jefferson '15 | Boys Division Championship Meet | 2012 |
