The Druk Padma Karpo School, where Amir's movie 3 Idiots was shot, also was washed away by the floods.
Amir met the principal of the school and promised to provide financial aid to the school and the other victims of Leh cloudburst.
"This is not how I would have liked to revisit Leh. I will contribute myself and I also want the people to contribute to the PM's Relief Fund," said Aamir.
Earlier, Prime Minister Manmohan Singh declared Rs 125 corer to the Leh relief fund on his visit to Leh.
"I appreciate the role of the media in telling the people of the country about the loss in Ladakh, but please don't scare people. Tell them it's safe to come here," said the Amir.
He also added, "People should come here because tourism is the backbone of the economy. I am standing here, I visited several villages here and it's perfectly safe to come to Leh."