McPharlin, who is not contracted for 2015, played his last game in round 20 against Geelong. He was subbed out of the match with a calf injury and despite desperate attempts to get back for the finals series he failed to return.
Following Fremantle’s semi-final exit at the hands of Port Adelaide, speculation surrounding the future of the 32-year-old key defender intensified, with many believing he may retire.
However, on Friday, Lyon told RSN that the 2012 All Australian was more likely than unlikely to continue.
"I think he's more likely," Lyon said.
"We've had some really positive conversations.
"At the end of the day, I've got a really strong relationship with Luke and he'll sort it out with his wife Kalinz.
"I think he's more likely than unlikely."
The Wash-Up: Fremantle
Lyon said he’d spoken to McPharlin about managing him carefully next year to avoid the injuries he’d suffered late in the last three seasons.
"In the conversations we have had, what we've spoken about is, we would manage him better," Lyon said.
"We've got faith in (fellow key defender) Alex Silvagni. So it might even be at the point where we commit to only 14 or 15 games for Luke and travel him less.
"Luke's in really good shape, but at the pointy end of the year in the past two years his body has fatigued and had some soft tissue (injuries).
"If we can manage that, he'll be in good shape and we'll be in good shape."
McPharlin missed both of Fremantle's finals in 2012 after injuring his hamstring.
He tore his calf in round 15 of 2013 and missed eight games before returning to play all three finals.
In 2014 he managed just 13 games due to several different injuries. He missed two weeks with a quad problem before the first bye and then missed three matches after suffering a medial ligament strain in his knee in round 12.
He returned in round 16 but did not play the next round due to calf soreness. He played the next three matches before the calf flared again, ruling him out of the remainder of the season.
The Dockers have declared themselves in the race for the services of James Frawley, with rumours of a $3 million five-year deal being tabled to the Melbourne defender.
Lyon said the club's list management committee would meet next week to discuss plans for the draft, trade and free agency period. He confirmed key position players would clearly be on the agenda.
"It would be key forwards and key backs but we did draft last year and the year before, young talls," Lyon said.
"We've got (Matt) Taberner coming through, young (Michael) Apeness. So they're the areas, key backs and key forwards, which you've either got to grow or go through free agency.
"We're more likely to grow them because they're hard to get, although we are speaking to James Frawley."
