The former Cranes skipper was appreciated for his unwavering and unselfish service to the country for the past 16 years.
The Mamelodi Sundowns custodian was invited by the Head of State on Thursday.
Museveni expressed his intentions to honour him, after his positive impact at the national team.
Onyango was also appreciated for what he has done for football at large in the East Africa country.
“Onyango has been a role model for many in Uganda, and I compliment him for what he has done,” Museveni said in his speech.
“As a government we will try to come up with a way of retaining our athletes here to nurture others.”
“We thank all the sportsmen and women for what they have achieved despite the fact the Government has not offered full support,” he added.
Onyango who was accompanied by his mother and sister appreciated the gift by the President.
He stated he opted to retire because he had served for long.
“I thank you, the President, for deciding to honour me with this amazing gift,” Onyango said.
“I also take this opportunity to thank all the Ugandans for their support.”
“However, I felt it was my time to retire. I have diligently served the country and it is time for others to get the chance as well,” he added.
He played for Cranes since 2005 until he announced he will not be part of the team anymore to focus on his club.