Johnston took the Saints to six finals during his time at the club having joined in 2008 and he leaves with the best wishes of chief executive Allan Robson.
"Nick has been an important person behind the scenes over the past few years and I'm sorry to see him leave us," Sky Sports News quotes Robson as saying.
"He has worked extremely hard to get our performance department into a place where it is the envy of the other Aviva Premiership clubs and at the cutting edge.
"However he now has a young family and wants to take some time to enjoy being a new father. I'd like to thank Nick for everything that he's done at Franklin's Gardens and wish him all the best for the future."
The Saints are currently second in the Premiership after five games.