The 67-year-old leaves Atalanta after nine years having transformed them from Serie A strugglers to consistent Champions League competitors.
Atalanta released a statement thanking Gasperini for his services as they start the process of finding someone capable of filling his shoes.
The club said: “After so many years spent together we felt it was our duty to respect his desire to seek new stimuli, knowing full well that our relationship will never end and that our mutual respect will never diminish.”
He now looks set to take charge of Roma, replacing the legendary Claudi Ranieri following his decision to retire from management.