Christianity in Chad arrived more recently than other religions, with the arrival of Europeans. Its followers are divided into Roman Catholics and Protestants (including several denominations) and collectively represent 45% of the country's population.

The Protestants came to southern Chad in the 1920s. The American organization Baptist Mid-Missions was the first Protestant mission to settle in the country in 1925 in Sarh. Missionaries of other denominations and nationalities soon followed. Many of the American missions were northern offshoots of missionary networks founded farther south in the Ubangi-Chari colony (now Central African Republic) of French Equatorial Africa (Afrique Equatoriale Franchise — AEF). The organizational ties between the missions in southern Chad and Ubangi-Chari were strengthened by France's decision in 1925 to transfer Logone Occidental, Tandjilé, Logone Oriental, and Moyen-Chari prefectures to Ubangi-Chari, where they remained until another administrative shuffle restored them to Chad in 1932.

In 1964, the Chadian Association of Baptist Churches was officially founded.

These early Protestant establishments looked to their own churches for material resources and to their own countries for diplomatic support. Such independence allowed them to maintain a distance from the French colonial administration. In addition, the missionaries arrived with their wives and children, and they often spent their entire lives in the region. Some of the missionaries who arrived at that time had grown up with missionary parents in missions founded earlier in the French colonies to the south. Many remained after independence, leaving only in the early and or mid-1970s when Tombalbaye's authenticité movement forced their departure.

The missionaries set up schools, clinics, and hospitals long before the colonial administration did. In fact, the mission schools produced the first Western-educated Chadians in the 1940s and 1950s. In general, the Protestant missionary effort in southern Chad has enjoyed some success. In 1980, after a half-century of evangelization, Protestants in southern Chad numbered about 80,000.

From bases in the south, Protestants founded missions in other parts of Chad. In the colonial capital of Fort-Lamy (present-day's N'Djamena), the missions attracted followers among resident southerners. The missionaries also worked among the non-Muslim populations of Guéra, Ouaddaï, and Biltine prefectures. There were estimated to be 18,000 Christians in N'Djamena in 1980.

Catholic presence is first recorded in 1663 through the work of Capuchin Franciscans, anteceding Protestant missions by more than 200 years, although permanent missions came to Chad later than their Protestant counterparts. Isolated missional efforts began as early as 1929 when The Holy Ghost Fathers from Bangui founded a mission at Kou, near Moundou in Logone Occidental Prefecture. In 1934, in the midst of the sleeping sickness epidemic, they abandoned Kou for Doba in Logone Oriental Prefecture. Other priests from Ubangi-Shari and Cameroon opened missions in Kélo and Sarh in 1935 and 1939, respectively.

In 1946 these autonomous missions gave way to an institutionalized Roman Catholic presence. This late date had more to do with European politics than with events in Chad. Earlier in the century, the Vatican had designated the Chad region to be part of the Italian vicarate of Khartoum. Rather than risk the implantation of Italian missionaries during the era of Italian dictator Benito Mussolini, the French administration discouraged all Roman Catholic missionary activity. For its part, the Vatican adopted the same tactic, not wishing to upset the Italian regime by transferring jurisdiction of the Chad region to the French. As a consequence of their defeat in World War II, however, the Italians lost their African colonies. This loss cleared the way for a French Roman Catholic presence in Chad, which a decree from Rome formalized on March 22, 1946.