The Scot, who had been working as David Moyes' assistant at Goodison Park, has agreed a three-and-a-half year deal with the club.
North End chairman Derek Shaw told the club's official website: "We're very pleased that Alan will be joining us, he's ready to have a crack at management.
He's got a reputation of being a top-notch coach, his work ethic is amazing. He's worked with David Moyes and I know the amount of games they take in, you see them all over the country.
Steve Cotterill, Paul Ince, Paul Jewell and Mike Newell had all been linked with the post made vacant by Paul Simpson's departure earlier this month.