President Yoweri Museveni said he and the American rapper held "fruitful discussions" on Monday about promoting tourism and arts.
The American rapper and his reality TV star wife have been vacationing in a national park in Uganda, where he is said to be recording music in a tent.
Uganda's presidency released photos of a hoodie-wearing West meeting Mr Museveni at the State House and exchanging gifts.
The president, one of Africa's longest-serving leaders, has been at the centre of unrest in recent weeks as Uganda's large youth population increasingly expresses frustration over unemployment.
Following the visit, he wrote on Twitter: “I thank Kanye for the gift of white sneakers. Enjoy your time in Uganda. It is the true Pearl of Africa.”
The visit comes less than a week after West made headlines by meeting US President Donald Trump at the White House .
The musician spoke excitedly on social issues, hydrogen planes, mental health, politics and other topics, while stunned reporters looked on.
"They tried to scare me to not wear this hat," West said of his red "Make America Great Again" cap. But, he said, "This hat, it gives me power in a way."