Tourism is the biggest foreign exchange earner in the East African nation, which is trying to lay to rest memories of a 1994 genocide in which 800,000 Tutsi and moderate Hutus were slaughtered by ethnic Hutu extremists.
Starting in August, the "Visit Rwanda" tourist board logo will be emblazoned on the left sleeve of all players in Arsenal's first, under-23 and women's teams, the government said in a statement.
Rwanda did not disclose how much it would pay, but it said the three-year deal would highlight its "growing numbers of wildlife including black rhino, lions, zebra, chimpanzees and the famous mountain gorillas."
The tourism deal is not the only link between Rwanda and the north London side. Many of Kagame's critics compare his prolonged stay in power to that of Arsenal manager Arsene Wenger, who retired this year after 22 years in charge.
Kagame, who posted a plaintive message this month about Wenger's departure from "my beloved Club Arsenal", came to power after the 1994 genocide and has recently changed the constitution to allow him to stay until 2034.
Arsenal chief commercial officer Vinai Venkatesham described the deal as an exciting partnership that would allow Rwanda to fulfil the ambitions of its tourist industry.
The country hopes to bring in $440 million (330.3 million pounds) this year from foreign visitors, many of whom will be coming to visit its population of endangered gorillas in forests along the border with Democratic Republic of Congo.
(Reporting by Clement Uwiringiyimana; editing by Elias Biryabarema, Larry King)
