The 28-year-old, who made 35 appearances for the Shrimpers in League Two last season, was handed a custodial sentence after being found guilty of perverting the course of justice in Basildon Crown Court, having supplied false details to avoid a speeding fine.
But the Essex club have offered their full support to their man.
"Southend United Football Club have today been made aware that Michael Timlin has received a custodial sentence for a period of 84 days in relation to traffic offences," a club statement read.
"The club have always found Michael to be a most professional and honourable person and believe the error of judgement leading to his imprisonment totally out of character.
"At the time of this statement the club does not have the full details but it will be our intention to stand by Michael to help and support him in anyway possible.
"The club will provide a further update when more information is available."
Timlin did not feature for the Shrimpers after he broke his leg against Leyton Orient in February and is currently out of contract, though stated his desire to stay at Roots Hall last month.