Resuming the program, which represents only a part of the halted aid, is one sign of warming relations between Washington and Islamabad.
Trump hosted Pakistani Prime Minister Imran Khan at the White House in July, and the US has several times welcomed Pakistani help in negotiations with the Afghan Taliban.
In January 2018, Trump froze the assistance, saying Pakistan was not doing enough to target bases of the Afghan Taliban and its affiliated Haqqani group.
According to a US State Department spokesperson, the freeze "authorized narrow exceptions for programs that support vital US national security interests."
The US administration "has approved the resumption of the International Military Education and Training (IMET) program for Pakistan as one such exception, subject to congressional approval," the spokesperson said.
US officials have long accused Pakistani agencies of collaborating with Islamist radicals including the Taliban, but they cite progress over the past few months.
Islamabad has denied such accusations and at the time called it "counterproductive" to threaten security aid, which Trump froze prior to Khan's election in August 2018.
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