Macken, 44, was previously in charge at Colne and Radcliffe, and succeeds Carl Macaulay following Witton’s relegation from the NPL Premier Division.
He said: “I am delighted to accept this opportunity to manage this club and I am looking forward to the challenge ahead at Witton Albion, a club with a very good history, passionate supporters and great volunteers who all work extremely hard for the football club.
“If we pull together and work hard, I am sure we can get this club back up the league.
Macken is well known from his playing days at Manchester City, Preston, Crystal Palace and Barnsley, amongst others, as well as for winning international caps for Republic of Ireland.
Witton’s acting chairman, Graham Wood said: “Jon has some exciting ideas for the future development of our club and we look forward to working together to bring competitive and entertaining football to our fans in the coming seasons.
“It is vitally important that the Witton Albion fans get behind our new manager and the new squad of players that Jon will be assembling over the next few weeks.”