Cooper first joined the Cockburn club in 2018, succeeding inaugural Dockers coach Michelle Cowan ahead of the club's third season in the competition.
Fremantle would secure second spot on the ladder thanks to a 6-1 record under Cooper before in his first year at the helm before bowing out of the finals in their only post-season appearance.
The following year the Dockers would secure the minor premiership under Cooper, who was named as the AFLCA's Coach of the Year for 2020.
The Dockers would remain contenders under Cooper through 2021 and the early 2022 season, while Season 7 tested his squad, who managed their first non-finals finish under the 48-year-old.
At the cessation of their most recent campaign, Fremantle confirmed Cooper's tenure would not be extended for another season.
“Trent Cooper will always hold a special place in Club history after guiding our AFLW team to an historic first finals campaign in 2019,” Dockers CEO Simon Garlick said.
“In five seasons, Trent took the team to the finals four times which is a significant achievement.
“We thank Trent for his passion and dedication to our Club.
“He and his wife Josie, along with their children Peyton and Allegra, will always be part of the Freo family."
Cooper thanked the club for the opportunity he was given across five years with the Dockers, stating he was grateful despite the "tough" decision.
“I have met some special people over my time here and I'm extremely proud of what we have been able to achieve together,” Cooper said.
“This is a tough moment for me because I work with an incredible group of people.
“I'm grateful for the support I've had along the way, whether that be from the Club, fans, our sponsors, the staff, my coaches, my players or my family, and it's something I will always cherish.”
Fremantle are set to commence a search for a new senior coach ahead of the 2023 AFLW season.