The two-time Brownlow medallist called time on his glittering 16-year career on Monday.
Knee, hamstring and calf injuries have kept the 33-year-old to just five games so far as the fourth-placed Dockers look to seal a spot in finals.
Fyfe says he is at peace with his decision.
"Retiring has been a conversation that has been ongoing for probably the last 12 months," Fyfe said in a club statement.
"It just feels like it's the right time.
"I'm just immensely grateful for what my AFL experience and playing with Fremantle has given to me.
"Knowing this is the end of my career, I leave with a sense of understanding that I don't need anything further, which is a really peaceful place to be."
Fremantle football boss Joe Brierty lauded Fyfe as one of the club's greatest players.
"Nat's legacy at the Fremantle Football Club will live on forever," Brierty said.
"When he arrived at the Club back in 2009, it was clear he had raw talent.
"With his decision to retire at the conclusion of our 2025 campaign, we know he will leave no stone unturned to make the most out of every moment left."
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