Museveni met with Kenyatta in State House, where they held bilateral talks on various issues affecting the East African region.
According to the presidency, the two leaders discussed the progress of the Standard Gauge Railway which is meant to connect all East African states.
Kenya is already constructing the second phase of its rail, while Uganda last week said it would begin working on its side soon, with a budget already in place.
The SGR is set to significantly shorten the time taken for goods to be transported across the East African states, also widely cutting cost.
Kenyatta and Museveni also discussed the continued deployment of AMISOM troops in Somalia.
They emphasized the need for the Somali government to build and strengthen its national army in order to boost security in the Horn of African country.
Museveni pledged to convene a meeting of Chiefs of Defence Forces from Troop Contributing Countries to discuss progress in the mission.
