| RK | Name | H/L | Time | Gap | Q |
|---|---|---|---|---|---|
| 1 | Kolesnikov Nikolai (2006)Russian Federation | 03:57.87 96.605% | - | D4 | |
| 2 | Babinich Egor (2007)Russian Federation | 04:00.20 96.848% | 00:02.33 | D5 | |
| 3 | Kovács-Seres Hunor (2006)DKSE Dunaújváros | 04:00.64 97.817% | 00:02.77 | D3 | |
| 4 | Pápai Olivér (2009)UNI Győri Úszó Sportegy. | 04:02.00 100.062% | 00:04.13 | D6 | |
| 5 | Kárpáti Máté (2008)Újpesti Torna Egylet | 04:02.60 99.336% | 00:04.73 | D2 | |
| 6 | Duca Stefan-Mircea (2006)BVSC-Zugló | 04:03.40 99.121% | 00:05.53 | D7 | |
| 7 | Grandpierre Krisztián (2007)Ferencvárosi Torna Club | 04:03.45 100.372% | 00:05.58 | D1 | |
| 8 | Poteczin Dániel (2006)Érdi Vízisport Kft | 04:03.48 98.355% | 00:05.61 | D8 | |
| 9 | Kaló Kristóf (2007)Egri Úszó Klub SE | 04:05.89 101.281% | 00:08.02 | T1 | |
| 10 | Kakuk Koppány Zéta (2008)Kaposvári Sportközpont és Sportiskola | 04:07.67 95.792% | 00:09.80 | T2 | |
| 11 | Baumann Marcell (2006)UNI Győri Úszó Sportegy. | 04:07.93 101.255% | 00:10.06 | ||
| 12 | Kaiser Dominik (2007)Újpesti Torna Egylet | 04:08.71 97.282% | 00:10.84 | ||
| 13 | Musa Márk (2007)Hód Úszó SE | 04:09.31 100.100% | 00:11.44 | ||
| 14 | Rajcsányi Boldizsár (2007)Lőrinc Swim Team | 04:11.17 101.860% | 00:13.30 | ||
| 15 | Palkovics Olivér (2007)Lőrinc Swim Team | 04:11.51 99.853% | 00:13.64 | ||
| 16 | Buda Levente (2008)UNI Győri Úszó Sportegy. | 04:12.06 96.718% | 00:14.19 | ||
| 17 | Spisák Bence (2008)Budaörsi Sport Club | 04:13.67 100.844% | 00:15.80 | ||
| 18 | Bercse Bence (2007)UNI Győri Úszó Sportegy. | 04:15.37 101.039% | 00:17.50 | ||
| 19 | Huszár László (2007)Ferencvárosi Torna Club | 04:17.25 98.943% | 00:19.38 | ||
| 20 | Bögözi Hunor (2007)Kaposvári Sportközpont és Sportiskola | 04:18.60 98.826% | 00:20.73 | ||
| 21 | Páva Olivér (2008)A Jövő SC | 04:19.02 97.450% | 00:21.15 | ||
| 22 | Csernyik Dániel (2006)Nyiregyházi Sportc.Nonprofit.Kft. | 04:24.82 97.033% | 00:26.95 | ||
| - | Deák Gergely (2007)A Jövő SC | DNS - | |||
| - | Nagy Bence (2007)Újpesti Torna Egylet | DNS - | |||