The 24-year-old, who signed for Wolves in September 2015 from Swindon Town, joins Gary Caldwell and his League 1-winning Latics side.
Byrne made his debut for Wolves at home to Brighton & Hove Albion in the 2015/16 season and went on to make 24 appearances for the club.
The winger joins a Wigan Athletic side who sit in 20th place in the Sky Bet Championship table after five games.
The Club would like to thank Nathan for his efforts during his time at Molineux and wish him well for the future.