Agafonov swam for his second time in the 100 m freestyle at the 2004 Summer Olympics in Athens. He achieved a FINA B-standard of 52.10 from the Russian Championships in Moscow. He challenged seven other swimmers in heat two, including 28-year-old Željko Panić of Bosnia and Herzegovina. He raced to fourth place by 0.17 of a second behind Panic in 52.92. Agafonov ended his third Olympic stint with a fifty-seventh-place effort in the preliminaries.