Kher took to Instagram to share a picture of himself accepting the prestigious Padma Bhushan award from Mukherjee in 2016 and expressed deep sorrow over his demise in the caption.
"Deeply saddened to know about the demise of Bharat Ratan Hon. Shri #PranabMukherjee. He was a compassionate politician, a great statesman and a wonderful human being," wrote Kher.
He further went on to share an anecdote from the time when he had met Mukherjee in Kolkata before he took charge as the President.
"Before he became the President of India I had the privilege of spending few moments with him in Kolkata. While shaking my hands he said,"I like your comedy in movies!" I was so thrilled. It was an honour to receive my #Padmabhushan from him. We will miss you #PranabDa. Om Shanti," the 'Saaransh' actor wrote.
Actor Ayushmann Khurrana, on the other hand, took to Instagram stories and paid homage to the late President by posting his picture and writing, "Purva Rashtrapati aadarniya Pranab Mukherjee ji ko bhaavpurna shradhanjali (My deepest tributes to respected former President Pranab Mukherjee."
Megastar Aamir Khan and actor Paresh Rawal also condoled the demise of the former President on Twitter.
While Khan tweeted, "Pranabda, rest in peace," the senior actor wrote, "Pranab Da AUM Shanti" on Twitter.
Mukherjee, 84, passed away on Monday at the Army Hospital (Research and Referral) Hospital where he was admitted earlier this month and had undergone surgery for the removal of a clot in his brain.
State mourning is being observed throughout the country from August 31 to September 6 as a mark of respect to the former President, who passed away on Monday.