The test is the latest in a series carried out by India and Pakistan since both demonstrated nuclear weapons capability in 1998.
The military said it had fired a Shaheen III surface-to-surface ballistic missile which can carry nuclear and conventional warheads within a range of 2,750 kilometers (1,700 miles).
"The successful flight test with its impact point in the Arabian Sea, validating all the desired parameters ... was aimed at validating various design and technical parameters of the weapon system," the military said in a statement.
The head of the Strategic Plans Division, Lieutenant General Mazhar Jamil, congratulated scientists and engineers involved on achieving a "significant milestone" which complemented the country's existing deterrence capability, it said.
Jamil asserted that "Pakistan desires peaceful co-existence in the region for which nuclear deterrence would further strengthen strategic stability in South Asia," Agence France Presse reported.
Pakistan last tested the Shaheen III on March 9 this year.
Relations between Pakistan and India -- which have fought three wars since independence from Britain in 1947 -- have always been fraught but soured further last August amid a rise in clashes along their borders and a row over a Pakistani diplomat meeting Kashmiri separatists.
On Wednesday India's Foreign Minister held talks with her Pakistani counterpart Sartaj Aziz in Islamabad on the sidelines of a regional summit on Afghanistan, where they jointly announced they would resume high-level peace talks.