The midfielder sustained the serious injury in the late stages of Tuesday night's 1-0 victory at Leyton Orient in the first leg of their Johnstone's Paint Trophy southern area final.
And a visit to a surgeon has confirmed Timlin has a displaced fracture of his tibia.
Southend physio Ben Clarkson told the club's official website: "We visited the surgeon and it was revealed that Michael would need to have it pinned and plated.
"It's in a plaster at the moment but we will be looking into the options available. It can't be left to heal unfortunately so it has to be worked on.
"It's a real blow for Michael and the team, but he's a strong lad and hopefully he will come back stronger on his return.
"Everyone here would like to thank the medical staff at Leyton Orient as well as those at Whitts Cross Hospital for their care on Tuesday night.
"I know Michael also wanted to say thank you to all the fans for their messages of support."