The 1,443-kilometer pipeline will transport crude from oilfields being developed in Lake Albert in northwestern Uganda to a Tanzanian port on the Indian Ocean.
"The approval (of the license) is another sign to demonstrate the joint commitment by the two countries to develop the EACOP project in a harmonized manner," Ugandan Information Minister Godfrey Kabbyanga told AFP.
The license was granted to the East African Crude Oil Pipeline Company Ltd, which is 62 percent owned by France's oil giant TotalEnergies, following cabinet approval on Monday.
Last year, TotalEnergies and the China National Offshore Oil Corporation (CNOOC) signed a $10-billion agreement to develop the Ugandan oilfields and build the pipeline.
Uganda's first oil is expected to flow in 2025 -- almost two decades after the reserves were discovered.
The government has vowed to plough ahead with the scheme despite the opposition and calls by the EU parliament last year for it to be delayed over rights concerns.
President Yoweri Museveni is due on Tuesday to officiate at the launch of drilling activities at the Kingfisher oil fields in Lake Albert operated by CNOOC.
Museveni has in the past hailed the project as a major economic boost for the landlocked country, where many live in poverty.
But the project has run into strong opposition from activists and environmental groups that say it threatens the region's fragile ecosystem and the livelihoods of tens of thousands of people.
It includes drilling in Murchison Falls, Uganda's largest national park on the shores of Lake Albert.
The lake, a natural border between Uganda and the Democratic Republic of Congo, lies atop an estimated 6.5 billion barrels of crude, of which about 1.4 billion barrels are currently considered recoverable.
Meanwhile, Uganda will host the 10th East African petroleum conference between May 9 to 11 this year to showcase East Africa as a "hotspot for hydrocarbon discoveries", Kabbyanga said.
The government is also undertaking studies to open other areas in the country for petroleum exploration, he added.