Mukherjee, who joins Naked with the title of group managing partner, will initially be based at the agency's Amsterdam office. He will partner with Jason Dawes, the former Adidas head of media, who runs Naked's Amsterdam operation.
The pair will work on developing an international element to Naked's Amsterdam offering, with the launch of the brand in Germany a priority. Naked also has a presence in Paris and the Nordic region.
Mukherjee joins Naked after leaving W&K in September last year. He had been at the advertising agency since 1999 and had focused on media initiatives for its Nike European and global football activity.
Mukherjee started his career 21 years ago at BMP, where he met most of Naked's founding partners. He is a close friend of Ivan Pollard, who joined Naked as its fourth partner in 2005.
Nigel Long, the chief executive of Naked, said: "Paul has proven global management experience, as well as being able to practice what Naked preaches. It's a rare combination and I'm sure he'll make an immediate impact."
Separately, John Harlow, a founding partner of Naked, is currently on sabbatical. It is unclear when he will return to the business.