The 40-year-old former New Zealand player is currently forwards coach at Clermont Auvergne and he previously held a similar position at Leinster.
Gibbes will work under director of rugby Les Kiss, while current head coach Neil Doak's future is unclear.
"The respect I have for Les as a coach and person was one of my main reasons for making this decision," said Gibbs.
Ulster are sixth in the Pro12 table and out of the European Champions Cup in what has been a largely disappointing season.
"Les sold his vision of where he wants to take Ulster over the next few years," added Gibbes.
"Ulster is a team that I know well, having come up against them on a number of occasions. The Clermont-Ulster games this season gave me an insight into the strengths of the squad and it's exciting to think that I'll be part of that environment from next season."
Gibbes, who joined Leinster in 2008 and won three Heineken Cups during his spell in Dublin, said: "With six years at Leinster and three at Clermont in the Top 14, I've been afforded many different experiences, working with some very talented coaches and players.
"I hope to apply what I've learned to the role at Ulster and my family and I are looking forward to integrating into a strong community in Belfast."
He moved to France in 2014 and was part of a coaching set-up that guided Clermont to the Top 14 and Champions Cup finals in his debut season.
"Jono's CV speaks for itself and I know that he's looking forward to joining Ulster and working with the team," said Kiss, 52.
"Since his retirement from playing, Jono has had an integral role in the coaching teams of two of European rugby's most successful sides.
"Jono's expertise as a forwards coach is obvious, however his wealth of knowledge in other areas of the game will be really important for us."
"A review of the coaching structure is ongoing ahead of next season and the appointment of Jono as head coach is the first part of that process.
"A further announcement will be made in the coming weeks, which will focus on getting the right balance in our coaching team."
Jono Gibbes is to become the head coach of Pro12 side Ulster on a two-year deal in the summer.