Clarke’s managerial career has covered nearly 700 games and he won promotion from League Two with Bristol Rovers in 2016 and Port Vale in 2022.
But his second spell at Rovers came to an end in December when he was sacked following a run of 10 straight league defeats.
He now joins a club in Tranmere who finished 21st, only two points clear of the drop zone, and had Andy Crosby and then Pete Wild – on a short-term basis – as managers during the 2025-26 season.
And he faces a busy summer ahead at Prenton Park with 12 players having departed at the end of the campaign.
Clarke added: “The chairman was very open with me about the fact that there is a big recruitment job to do.
“We have fewer players under contract than usual at this time of year, but I see that as an attraction because the job is much harder when you are inheriting a large number of players who are already under contract but may not fit with your style or be the type of characters you want in the building.”