Relations have been strained for years amid accusations that both Khartoum and Kampala support rebel groups in each other’s country.
But after South Sudan won independence from Sudan in 2011, ties improved slightly, with Ugandan President Yoweri Museveni visiting Khartoum last year.
“President Omar al-Bashir has left for a two-day visit to Uganda,” the official SUNA news agency reported.
Sudan has previously accused Uganda of backing rebel groups in the south before independence as well as in Darfur.
Kampala for its part has accused Khartoum of supporting the Lord’s Resistance Army, a rebel group from Uganda.
Even now several leaders of Sudanese rebel groups from Darfur reside in Uganda.
Experts say Bashir’s visit is part of his strategy to enhance relations with neighbouring countries in an attempt to curb their influence on rebel groups in Darfur and other conflict-hit regions of Sudan.
Bashir was indicted by the ICC in 2009 for alleged war crimes in Darfur, which he denies.
Darfur has been gripped by conflict since 2003, when ethnic minority rebels rose up against Bashir, complaining that his Arab-dominated government was marginalising the region.
Bashir launched a brutal counter-insurgency, in which at least 300,000 people have been killed and 2.5 million forced to flee their homes, according to figures released by the United Nations.
He is accompanied on his visit to Kampala by Foreign Minister Ibrahim Ghandour and the head of the powerful National Intelligence and Security Services (NISS), Mohamed Atta, along with other senior Sudanese officials.
What a shame? This shows that Mr museveni is isolated by the western world which has been his strong covert supporter. Only dictators have managed to attend the ceremony, people like mugabe,Bashir, Ali bongo well known violators of human rights and suppresers of freedom, the ceremony was exclusive to criminals rather than people of reputation. No western democracy present, what does that indicate? It can only indicate that dictatorship has no space in todays world and can not be entertained by reputable people, with excepton of futune seekers and opportunistic individuals, museveni is quickly killing off the east africa by iputing his dictatorial tedencies in new leaders such huhuru and ruto, magufuli pombe is the new victim in the queue, kagame was done long aga, kiir is just following the museveni winds, therefore this ceremony is irrelevant and luck substance and popular support from both the democratic communities and the local society with a few exceptions categorised by thieves that Rob the nation and scared of change. Ugandans should vehemently reject this position, we are not ready to smile @ dictators for return of favours.