His famous quotes and photos were posted on Facebook to pay tribute to him.
"Hearty tribute to Abdul Kalam, former President of India. Deep condolence to the government and people of India," said former deputy prime minister and minister for foreign affairs Narayan Kaji Shrestha, in a message.
"He never got old. That was his charisma. What a hero - Abdul J Kalam ! love you !" a woman journalist Anjali Subedi wrote on her Facebook wall.
Nepal's Prime Minister Sushil Koirala expressed deep sorrow over the demise of Kalam saying: "I am saddened to hear the news of passing away of Kalam."
Koirala expressed his condolence to Indian Prime Minister Narendra Modi, government of India, relatives of Kalam and Indians on behalf of the government and people of Nepal.
Koirala also recalled Kalam's contributions in leading India on the path of scientific advancement and progress.
Kalam died in Meghalaya on Monday following cardiac arrest while delivering a lecture in the IIM-Shillong.
Nepal media widely covered news of his death in Tuesday's edition.
OneIndia News (with inputs from agency)