They said that they would raise their son together while still working on joint projects.
The statement read, "In these fifteen beautiful years together we've shared a lifetime full of joy, laughter and experiences."
Khan, 56, and Rao (47), first met in 2001 and were married four years later.
They stated that they wanted to "begin another chapter in our lives, not as husband and wife but as co-parents for each other".
Khan is a Bollywood actor who has enjoyed a long career that spans nearly 50 years. He has a huge following both in India and overseas, particularly in China.
Khan, a Hindu and a critic of the ruling BJP party, said Khan that he and Rao had no intention to leave the country.
He stated that those who called him anti-national and shouted obscenities at him for speaking their hearts out were only proving his point.
Khan was previously married to Reena Dulta and they have two children.