The 23-year-old injured his posterior cruciate ligament on New Year's Eve at the Falls Music and Arts Festival in Victoria and was initially ruled out for eight weeks of pre-season training.
Despite the interruption, Lyon believes Clarke will be available for the Dockers' opening match of the season on March 14.
"I expect him to be playing round one," Lyon said.
"Unfortunately sometimes people are going to get hurt. It's not ideal for us. We're in the business of healthy bodies but we all live and learn."
Lyon was not as confident about Anthony Morabito. The explosive midfielder is coming off his third knee reconstruction and is again being managed through the pre-season.
Lyon has no timeframe on when Morabito will return.
"The reality of Anthony is he is progressing well," Lyon said.
"At the right time Anthony will speak for himself. We're still controlling some of his drills just to look after him. There's no definitive time."
The likelihood is that Morabito will make a cautious return through the WAFL for Peel Thunder before the 22-year-old is considered for senior selection.
"I think that’s going to happen," Lyon said.
"He's missed three years of AFL football.
"I think it would be a natural progression for him."
Kepler Bradley and Jonathon Griffin are also returning from knee reconstructions and Lyon has been impressed with Bradley's recovery as he is in full training with the exception of some contact drills. Griffin is running freely but is still some weeks from joining the main group.
Lyon is pleased with the overall health of his squad. Alex Silvagni and Stephen Hill have trained away from the main group this week due to some muscle tightness.
New recruit Colin Sylvia will join the main group on Monday having worked through a managed program to get him up to speed.
"He's [Sylvia] had some slight back tightness," Lyon said.
"He was in an unfortunate position that Melbourne finished a lot earlier than we did so he had an extended break which put more pressure on him. So he's had to work hard to catch that up."
The Dockers first NAB Challenge match is four weeks away but Lyon is looking further ahead.
"We've got the honour of opening up the season in Melbourne, one which we're very excited about. We've earned that right," Lyon said.
"That's our number one focus.
"We're certainly not going to get caught up in any predictions. We've never done that before. We focus on the hard work and paying the price now and the results will follow."
