Prime Minister Sheikh Hasina along with her senior cabinet colleagues saw him off at the Hazrat Shahjalal International Airport.
Mukherjee was conferred with an honour for his role in Bangladesh's independence in 1971 on the second day of the tour.
The premier Dhaka University conferred on him a honorary law degree during the visit.
He held talks with his Bangladesh counterpart Zillur Rahman while Prime Minister Sheikh Hasina and several of her senior colleagues separately called on him to review bilateral relations.