Antonio Ereditato, leader of an Italian project dubbed Opera working between particle labs at CERN in Switzerland and Gran Sasso in central Italy, quit after the results were disproved amid reports of discontent among his team, the Italian Nuclear Physics Institute said.
Some members of Opera had wanted Ereditato to resign after a repeat experiment determined the neutrino particles didn't exceed light speed, the BBC reported.
Results of the initial test shocked the world, threatening to upend a century of physics theory based on the speed of light as the universe's absolute speed limit.
Speaking at the time, Ereditato called for "caution" because of the "potentially great impact on physics" of the result.
An experiment this month by a different group at the same Italian laboratory recorded neutrinos traveling at precisely light speed.
A spokesman for the Icarus group running the repeat test said he wasn't surprised by the result.
"In fact I was a little skeptical [of the first experiment] since the beginning," he told BBC News.
Ereditato has offered no comment on his decision to step down from his position with the Opera team, the BBC said.