"Taking this role at Plymouth Argyle feels like the perfect next step in my career and I would like to thank the chairman and board for the faith they have shown in me," Rooney said.
"This is an opportunity to be part of an exciting project. I look forward to helping to build a squad of players to play expansive football and to entertain the Green Army.
"I have experienced first-hand how talented the existing group of players is here and also the incredible atmosphere at Home Park.
"The club is on an exciting long-term journey, with a progressive plan in place. I am grateful for the opportunity to be part of it."
Argyle chairman Simon Hallett said: "Throughout the interview process, Wayne showed himself to be a passionate, intelligent, and knowledgeable candidate with an appetite to prove himself and develop his managerial career.
"So much so, that he reached out to the board when we started this process and was attracted by the project at hand and showed a real plan on how to lead the football club forward.
"His ambitions and aims match ours perfectly and we feel he is the perfect candidate to provide the exciting and attacking brand of football that we all like to see and help us achieve the club's mission."