The 85-year-old pontiff will visit Kinshasa during his trip to the DRC from January 31 to February 3.
He will then be joined by the Archbishop of Canterbury, Justin Welby, and the Moderator of the General Assembly of the Church of Scotland, Iain Greenshields, in heading to Juba in South Sudan from February 3-5.
It will be the pontiff's fifth visit to the African continent since being elected head of the worldwide Catholic church in 2013.
The pope's trip to the two countries, both plagued by violence, had initially been planned for July this year.
But it was postponed "at the request of his doctors", the Vatican said at the time, as the pope underwent treatment for knee pain.
There had also been concerns about security on the trip, according to Italian media reports.
The pope -- who in recent months has used a wheelchair -- had initially planned to visit Goma, in the war-torn east of DRC, but this stop has been removed from the new program.
About 40 percent of the estimated 90 million inhabitants of DRC are Catholic. Another 35 percent are Protestant or affiliated to Christian revivalist churches, nine percent are Muslim and 10 percent follow the Kimbanguist Congolese church.
The country has a secular government, but religion is omnipresent in most people's lives and the Catholic Church in particular has at times played a leading role in local politics.
South Sudan, the world's newest nation, has suffered from chronic instability since independence in 2011, including a brutal five-year civil war.
The pope's trip will be the 40th abroad of his papacy.