| Lane/Order | BIB | ATHLETE | Seeding Time | Note | |
|---|---|---|---|---|---|
| 1 | 127 | POLI | SAMUEL RAJ A/L DANIEL | 49.97 | q |
| 2 | 281 | UPSI | MUHAMMAD SYAKIR DANIEL BIN FAUZI | 49.89 | q |
| 3 | 223 | UPM | DANISH ZUHRI BIN DAZARI | 49.52 | Q |
| 4 | 108 | KKMAS | YUSRY BIN MOHAMMAD SAIFULLAH | 48.70 | Q |
| 5 | 219 | UPM | AHMAD AMIR AIMAN BIN MOHD KAMARUDDIN | 49.14 | Q |
| 6 | 202 | UMS | MUHMMAD KHALIL BIN HELMI | 49.39 | Q |
| 7 | 236 | UPM | MUHAMMAD AIDIL AZHAR BIN AZRUL HISYAM | 49.47 | Q |
| 8 | 266 | UPSI | EMMET ZARIQ SHAH BIN AZRUL IZAHARRUDIN SHAH | 49.58 | Q |