| RK | LN | Name | Time | Gap | FINA | Q? |
|---|---|---|---|---|---|---|
| 1 | 4 | Trencsényi Zsombor (2015)Debreceni Sportc. SI | 42.60 | - | 226 | |
| 2 | 3 | Molnár-Szalai András Béla (2015)Budapesti Honvéd SE | 45.90 | 03.30 | 180 | |
| 3 | 0 | Fehér Illés (2015)Gigászok SE | 48.81R:0.68 | 06.21 | 150 | |
| 4 | 5 | Borbély Zalán (2015)Clubul Sportiv Crisul | 49.19 | 06.59 | 146 | |
| 5 | 1 | Kovács Ármin (2016)Miskolci Sportiskola | 49.27 | 06.67 | 146 | |
| 6 | 2 | Büki Norbert János (2016)BVSC-Zugló | 49.92 | 07.32 | 140 | |
| 7 | 7 | Gere-Farkas Botond (2015)BVSC-Zugló | 51.02 | 08.42 | 131 | |
| 8 | 9 | Buzás-Főzy Zsombor (2016)BVSC-Zugló | 51.28 | 08.68 | 129 | |
| 9 | 8 | Kónya Kristóf Noé (2015)BVSC-Zugló | 51.44 | 08.84 | 128 | |
| 10 | 6 | Váradi-Vintner Huba (2015)KSK Delfin Klub | 52.34 | 09.74 | 121 |