The film, also starring actress Kajol, centres around a Muslim man (Shah Rukh) from India with Asperger's Syndrome (a form of autism), who travels across the US to meet President Barack Obama, after his world falls apart due to 9/11 terror attacks in the country.
Coelho, 67, took to Twitter to praise the Karan Johar-directed hit.
"My name is Khan" is the best movie I watched this year. @karanjohar @iamsrk Congrats for "My name is Khan". I wish we could see more of your movies in Europe. I had to wait 6 yrs to watch this!" he tweeted.
Johar, 43, was also quick to revert to the author. "What an honour sir!!! Thank you so much!! @iamsrk" he wrote.
The movie, jointly produced by Johar's Dharma Productions and Shah Rukh's Red Chillies Entertainment, was screened as a part of the 60th Berlin International Film Festival's official selection in 2010.
It did well at the box-office and also received critical acclaim.