At the 2008 Summer Olympics in Beijing, Rubacek qualified for the second time in the men's 100 m butterfly, by clearing a FINA B-cut of 53.71 from the European Championships in Eindhoven, Netherlands. He challenged seven other swimmers in the fourth heat, including three-time Olympians Ioan Gherghel of Romania and Juan Veloz of Mexico. Rubacek raced to fourth place by five hundredths of a second (0.05) ahead of Veloz, breaking a new Czech record of 53.53 seconds. Rubacek failed to advance into the semifinals, as he placed forty-second out of 66 swimmers in the preliminaries.