At the 2004 Summer Olympics in Athens, Stojanovska extended her program, swimming in three individual events. She posted a FINA A-standard of 2:13.01 (200 m butterfly) from the European Championships in Madrid, Spain, allowing her to include 200 and 400 m freestyle in her event line-up. On the second day of the Games, Stojanovska placed twenty-seventh overall in the 400 m freestyle. Swimming in heat two, she cleared a 4:20 barrier by posting a time of 4:19.39 to take a fourth seed over Jamaica's Janelle Atkinson. The next day, she finished thirty-fourth overall behind Czech Republic's Jana Myšková by 0.02 of a second in the morning's heats of the 200 m freestyle with a time of 2:04.64. In her final event, 200 m butterfly, Stojanovska ended her Olympic run with a twenty-sixth-place effort, failing to reach the semifinals for the fifth straight time since 2000. Swimming in heat three, she rounded out a field of eight swimmers to last place with a time of 2:16.51, nearly four seconds off the national record held by Mirjana Boševska.