The "Shaheen 1" missile, which has a range of up to 700 km, meaning it can reach arch-enemy India, was launched on Wednesday morning from a secret location.
"We have successfully test-fired the Shaheen 1," said military spokesman Major General Shaukat Sultan. "It can carry all kinds of warheads."
Shaheen 1 (meaning Falcon) can carry any type of warhead.
"The test is part of the ongoing series of tests of Pakistan's indigenous missile systems," a military statement said. "All technical parameters required to be tested were successful validated."
The test-firing comes five days after Islamabad test-fired the short-range Ghaznavi missile which India dismissed as nothing special.
The launch is the first in the region since last spring's tit for tat ballistic missile tests between the nuclear powers.
It also coincides with Pakistani Prime Minister Zafar Allah Khan Jamali's visit to the US, where he is asking for US help to redress what Islamabad sees as a conventional arms imbalance in the subcontinent.
Pakistan says the tests have nothing to do with simmering tensions with New Delhi.
Tensions between the arch-rivals eased several months ago, but hoped-for talks never materialised and Pakistani and Indian leaders have since traded accusations.