Essendon superstar Bonnie Toogood will miss the majority of the AFLW season after scans confirmed she suffered a knee strain during a sickening collision with Bombers teammate Amber Clarke.

Toogood will be sidelined for up to eight weeks after hurting her MCL when running into Clarke during the second quarter of Essendon's round-one defeat to Fremantle at Windy Hill on Saturday.

Key forward Toogood was steaming forward to take a mark inside 50 when she collected Clarke, who had run into her path seemingly completely unawares.

The pair clashed heads, then Clarke's head bounced on the ground when she landed. 

Play was stopped as medics cared for Clarke, then took her from the field on a stretcher.

Meanwhile, Toogood was visibly distraught on the sidelines and had treatment on her knee.

Essendon led by eight points at the time — after Daria Bannister kicked the opening goal on return from an ACL tear — but appeared rattled by the incident.

Clarke was concussed in the incident, but she was assessed in hospital on Saturday night and she avoided any neck damage or facial fractures.

"It's extremely unfortunate for Bonnie and Amber to have to spend time on the sidelines," Essendon's medical boss Megan Smith said.

"The incident was a heavy clash between the two players, with both showing extreme commitment to the ball.

"While we are disappointed that Bonnie will be out for a significant part of the season, we are relieved that there is no damage to her ACL.

"Bonnie will commence rehab with the aim of returning later in the year."

Toogood's absence is a major blow for Essendon's hopes of building on a breakthrough finals appearance last season.

Essendon are not putting any time line on Clarke's return, but she could technically be available for the Bombers' round-three match if she exits the concussion protocols on time.

AAP