He was presented a 150-men Tri-Services Guard of Honour.
He also flagged off the inaugural flight of Alliance Air from Shirdi to Mumbai.
Apart from Alliance air, two other Airlines will be operating flights from here between Mumbai and Shirdi.
President Kovind, after inaugurating the Airport, said this infrastructure development will create new employment opportunities in the area.
The president also inaugurated the Centenary Celebrations of Samadhi of Shri Saibaba at the Sai Mandir in Shirdi.
Chief Minister Devendra Fadnavis was also present here on the occasion. (ANI)