Clark has taken on the role with the Seasiders sitting at the bottom of the Championship table after losing 10 of their 14 league fixtures.
"I am absolutely delighted," Clark told the club's official website. "The main objective is to try and keep the club in the Championship and build from there. It is a big challenge because of our position in the league but it's a challenge that can be overcome.
"It's one that if we achieve what we set out to achieve, which is to stay in the league, it will be a tremendous feat by the whole group. I'm very confident with the players I've got here, in what we can do going forward, that we can achieve those goals."
Chairman Karl Oyston added: "We needed someone with experience of the Championship and that's what Lee brings to the club. Lee's done remarkably well in a difficult background at Birmingham.
"We needed someone to come in and organise us properly and bring in the structure, approach and positivity that we've been lacking. Results have demonstrated that. Lee is bright and positive and we're happy to support his plans for the squad moving forward."
Clark helped keep Birmingham in the Championship during their relegation battle last season.