The 25-year-old - who has missed the entire 2014 campaign with a serious Achilles injury - will retain control of the one-day side as well as taking over the County Championship job from Stephen Peters.
David Willey will take on the vice-captaincy role.
Peters relinquishes the job as leader in the four-day cricket after a summer that has seen Northamptonshire relegated from Division One of the County Championship without registering a win.
Wakely said: “I am completely honoured to have been asked to captain.
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“It is something I have wanted to do ever since I came to the club as a 13-year-old.
“I still have a lot I want to achieve with my own career and after a very frustrating year for me with my injury I cannot wait to get back playing.
“The responsibility of captaincy is something I have always loved and I hope I can play my part as we rebuild over the next few years.
“I will do everything in my power to make this club successful and I am excited about the challenge.”
Head coach David Ripley, meanwhile, believes the Wakely/Willey partnership is one that can take the County forward over several seasons.
He added: “It’s an exciting opportunity for Alex and David to shape the future of Northants Cricket in the coming years.
“The cricket management team believe it’s time for a change in direction and to take a longer term view as we look to bring success back to the cricket club”.
“Stephen captained the side for two seasons and he was instrumental in shaping the changes in attitude and structure that led the club to possibly it’s most successful season in 2013.
“I would like to thank him for his support and I look forward to welcoming Alex back to his leadership role and building on his impressive start in 2013.”