Penney has been Head Coach of Canterbury since 2006, and last season took them to their fourth straight ITM Cup national provincial title.
He also has Super Rugby coaching experience with the Crusaders where he was assistant coach in 2005 when they won the Super 12 title and he has maintained his involvement with the Crusaders as Development Squad Coach.
A former Canterbury Academy Manager, Penney will coach the defending World Champion New Zealand Under 20 side during next month's IRB Junior World Championship in South Africa and he is expected, pending a work permit, to arrive in Munster in mid July for the start of a two-year contract.
Commenting on the appointment Munster CEO Garrett Fitzgerald said: "We conducted a thorough search to find a replacement for Tony McGahan and were delighted with the calibre of the candidates. Rob Penney's record speaks for itself and we look forward to welcoming him to Munster."
Canterbury Rugby Football Union CEO Hamish Riach said: "Rob has been a great servant for Canterbury rugby. We are very sorry to lose a talented coach, but this is a fantastic opportunity for him and we wish him all the best."