The 44-year-old's arrival comes a day after Marti Cifuentes officially left the club, having been placed on gardening leave following the penultimate game of the season.
The second-tier side finished 15th in the table but won only two of their final 12 games under Cifuentes.
Stephan, 44, won the French Cup with Rennes in 2019.
"I feel very proud and excited to join QPR," he said.
"QPR is a historic club with strong values and passionate fans, so I feel honoured. I wanted to come here because I know there's a lot of passion around the club and around the team, and I feel very lucky to discover that."
CEO Christian Nourry said: "Julien's track record of developing young players into world-class talent was a major factor in our decision to appoint him.
"Alongside this, both at Rennes and Strasbourg he achieved historic league success."