The 20-year-old native of Bern, Switzerland is listed as week to week, the NHL team announced Thursday.
"I was skating and my left skate seemed to have caught a rut in the ice and my legs kind of went into a splits position," Baertschi said in a release. "I felt pain immediately and left the ice to have it checked. It's very disappointing to learn that it's a hip flexor injury that will keep me out of the lineup."
Baertschi had three goals in five games last season for Calgary. He spent most of the season with the Portland Winterhawks, recording 94 points (33-61) in just 47 games with the Western Hockey League club.
Baertschi has yet to record a point in four games with Calgary this season.
"I've started treatments and plan on working very hard at getting back to 100 per cent as quickly as possible so I can help our team be successful and win games," he said.