The decision came with tensions simmering between the two arch rivals over Kashmir.
It is the third time in recent weeks that Islamabad has refused to allow Indian leaders to use its airspace.
Requests by Indian President Ram Nath Kovind and Modi were turned down last month.
"Indian Prime Minister wanted to use our airspace but we denied permission in the perspective of black day being observed by Kashmiris today to condemn Indian occupation and ongoing grave human rights violations in Indian-occupied Kashmir," foreign minister Shah Mehmood Qureshi said in a statement.
He said the Indian high commissioner (ambassador) was being informed about the decision.
Qureshi did not disclose Modi’s destination but a senior Pakistani official told AFP the Indian prime minister had sought permission to use Pakistan’s airspace to travel to Saudi Arabia, where he is due to attend an investment summit.