He is due to arrive in Nairobi at about 5 p.m.
"We are living at a time when religious believers, and persons of goodwill everywhere are called to foster mutual understanding and respect, and to support each other as members of our one human family," the pope said in a pre-trip message.
Africa's Catholic church is growing fast with an estimated 200 million adherents in 2012, a figure expected to reach half a billion in 2050. In Kenya, about 30 percent of the 45 million population are baptized Catholics, including President Uhuru Kenyatta.
"We are ready to receive him," Kenya's inspector general of police, Joseph Boinnet, told reporters. "Security arrangements have been put in place, right from arrival." Kenyan media has said at least 10,000 officers would be involved.
Kenya has been targeted by a spate of attacks by Somalia's Al-Shabab in the past two years that have killed hundreds of people. In April, the group claimed responsibility for a massacre at Garissa University College that left at least 147 people dead. In 2013, an assault by Al-Shabab gunmen on a Nairobi shopping mall killed 67 people.
The pope will also seek to heal ethnic rifts that have long plagued Kenya.
"Pope Francis' visit to Kenya will be focused on inclusivity and reconciliation in relation to ethnic and religious tolerance, peace and stability," Kenyan presidential spokesman Manoah Esipisu said.
The pope is scheduled to visit the Nairobi headquarters of the United Nations on Thursday and is expected to address climate issues.
In Uganda, where police said they would deploy 12,000 officers for the visit, the pope is expected to hold Mass on Saturday and then address young people.
The third leg of the papal trip is to the Central African Republic. Dozens of people have been killed there since September in violence between Muslim Seleka rebels and Christian anti-balaka militias.
His schedule in Bangui, the capital, includes a visit to a mosque in one of the most dangerous districts. French officials have hinted heavily that the Vatican should consider scrapping the Bangui leg of his trip or at least scaling it back.
Al Jazeera with wire services