A high-level delegation led by Somali president, Mohamed Abdullahi Farmajo travelled out of the country on Monday.
Somali head of state received an official invitation from his Burundian counterpart, Pierre Nkurunziza.
His visit follows after Bujumbura objected to a proposal to withdraw about a thousand troops serving under the African Union peacekeeping mission in Somalia (AMISOM)
The two leaders are expected to discuss the bilateral relations between the two states and other related mutual interests.
The Federal Government of Somalia said it is committed to fully cooperate with African states on issues of concerns in the areas of the economy, diplomacy, and security.
Burundi troops are among first to arrive in Somalia in 2007 alongside Ugandan People Democratic Forces (UPDF) as part of AMISOM.