The 56-year-old will act as number two to Pat Fenlon, having worked for two years under Kenny Shiels, with whom he won the Scottish Communities League Cup in 2012, before his fellow Northern Irishman left Killie by mutual agreement earlier this week.
Nicholl, who won 73 caps for Northern Ireland, was also assistant at Aberdeen for five years from 2004 and 2009 and he has also managed at Millwall, Raith Rovers and Cowdenbeath.
Fenlon said: "I am delighted to have such an experienced coach as my assistant. Jimmy has a deep knowledge of the game and of Scottish football in particular and will be a great asset to the club.
"He is particularly good in the development of young players and this is another important factor for the club."
Nicholl said: "When Pat spoke of his plans for the club it was an easy decision for me.
"I am delighted to be his assistant and hope to contribute to the on-going development and success of one of Scotland's leading clubs."