In July 1890, the Holy See made the decision to Agra, resulting in the establishment of the Rajasthan Mission. This new unit was entrusted to the Capuchin Fathers of the Paris Province, who operated under the supervision of the Archbishop. In March 1892, the Rajasthan Mission was officially recognized as the Prefecture Apostolic of Rajputana. Then, in 1913, the Prefect at the time, Rt. Rev. Fortunatus Henry Caumont, OFM. Cap., was appointed as the first Bishop of Ajmer. On March 11, 1935, certain parts of the Dioceses within the present state of Madhya Pradesh were separated to form the newly erected Prefecture Apostolic of Indore.
On May 9, 1949, the Diocese was transferred to the care of the Diocesan clergy. Subsequently, on June 21, 1951, the Holy See issued a decree that transferred Bandikui, including its sub-station Alwar, from the Agra Archdiocese to the Ajmer Diocese for geographical and administrative reasons. However, the Agra Archdiocese retained jurisdiction over the districts of Bharatpur and Dholpur.
Another decree from the Holy See, dated May 13, 1955, led to a change in the name of the diocese to Ajmer-Jaipur. Additionally, by a decree from the Sacred Congregation for Evangelisation of People (Prot.no.1332/81, dated March 11, 1981), the civil district of Mandasaur was transferred from the jurisdiction of the Diocese of Ajmer-Jaipur to the Diocese of Indore. On December 29, 1984, the Diocese of Ajmer-Jaipur was divided, forming a new diocese called the Catholic Diocese of Udaipur. This new diocese encompassed the districts of Bhilwara, Chittaurgarh, Udaipur, Dungarpur, Banswara, and Thandla tehsil. The Holy Father appointed Rt. Rev. Joseph Pathalil as its first Bishop.
Through a mutual agreement between the diocesan bishop and the Superior General of the Little Flower Congregation, Cochin, on April 25, 1986, the districts of Sri Ganganagar, Hanumangarh, Churu, Bikaner, Jaisalmer, Jhunjhunu, Karoli, and Sikar were entrusted to the Little Flower Congregation for the purposes of evangelization, pastoral ministry, and development on a permanent basis. Finally, on July 20, 2005, the Holy Father Benedict XVI issued a decree that bifurcated the Diocese of Ajmer-Jaipur, creating a new Diocese known as the Catholic Diocese of Jaipur. This new Diocese included the districts of Jaipur, Alwar, Bikaner, Churu, Dausa, Sikar, and Sri Ganganagar. Most Rev. Oswald Lewis was appointed as the Bishop of the New Diocese, while the mother Diocese was renamed the Diocese of Ajmer.