The visit comes as the Islamic republic tries to shore up diplomatic support to ease its international isolation, with Raisi also due to travel to Uganda and Zimbabwe this week on the first Africa tour by an Iranian leader in 11 years.
In addition to meeting Kenyan President William Ruto, Raisi will head to Uganda later Wednesday for talks with his Ugandan counterpart Yoweri Museveni and see Zimbabwean President Emmerson Mnangagwa on Thursday.
Africa has emerged as a diplomatic battleground in recent months, with Russia and the West also trying to court support over Moscow's invasion of Ukraine, which has had a devastating economic impact on the continent, sending food prices soaring.
Western powers have also sought to deepen trade ties with the continent, along with India and China, which has been on an infrastructure spending spree in Africa.
Raisi described his visit to Kenya as "a turning point in the development of relations between (the) two countries."
He said his talks with Ruto reflected "the determination and resolve of both countries for expansion of economic and trade cooperation, political cooperation, cultural cooperation."
Ruto described Iran as "a critical strategic partner for Kenya" and said the two governments had signed five MoUs (memoranda of understanding) focusing on areas including information technology, investment promotion and fisheries.
"These memoranda will enhance and further deepen our bilateral relations for sustainable growth and development between our two countries."
Ruto told reporters that Raisi had also shared plans for Iran to set up a plant in the port city of Mombasa "to manufacture an indigenous Iranian vehicle that has now been given the Kiswahili name, 'Kifaru', meaning rhino."
According to Iran's official IRNA news agency, Raisi is heading a delegation that includes the foreign minister as well as senior businesspeople.
Iranian foreign ministry spokesman Nasser Kanani earlier expressed optimism that the three-day trip could help bolster economic and trade ties with African nations.
He also said on Monday that Tehran and the African continent share "common political views," without elaborating further.
Iran has stepped up its diplomacy in recent months to reduce its isolation and offset the impact of crippling sanctions reimposed since the 2018 withdrawal of the United States from a painstakingly negotiated nuclear deal.
On Saturday, Raisi welcomed Algerian Foreign Minister Ahmed Attaf in a bid to boost ties with Algiers.
Last week, Iran became a member of the Shanghai Cooperation Organisation (SCO), which includes Russia, China and India.
In March, Tehran agreed to restore ties with regional rival Saudi Arabia under a China-mediated deal. It has since been looking to re-establish relations with other countries in the region including Egypt and Morocco.
In June, Raisi undertook a Latin American tour that included Venezuela, Nicaragua and Cuba before a trip to Indonesia.