The soul of Bishop Cotton School lies in the chapel. One of the best preserved chapels in the country, with beautiful stained glass, polished pews, parquet flooring, pulpit and grand piano all intact. Every old boy who visits the chapel is touched most within this  hallowed house of God transcending religion and whispers reverently “its looking even better than our time”.

The original school chapel was built by Major Innes, RE at a cost of about Rs.50,000/- and was consecrated on 21st September 1871. The current service register goes back to 9th March, 1930. In the old service register there is a brief and poignant entry under the date 7th May 1905, “In the afternoon the school was burnt down…” Only the big Bible dated 1894 and the brassware were saved. The chapel was rebuilt and used again from 3rd April 1908. On entering you are faced by the dominating huge stained glass picturing the Good Shepherd. The original Bishop Cotton banner was consecrated in 1925 and is framed on the left wall. The fine communion rail was presented in memory of G.E.H. Ferry, a school master in 1914. Near the alter steps is the Foundation Plaque in copper, a replica of the marble one at the entrance of the chapel. Further ahead on the same side is a marble plaque dedicated to Old Cottonians who lost their lives in World War II. The pipe organ was installed in 1929. In 1921-22 the seating arrangements, which were parallel to the side wall, were altered to the present seating, accommodating more boys. In 1935 the chapel was extended. The Italian marble font and three stained glass windows were gifted by  the Viceregal Lodge Chapel, Simla to the school in 1966 and installed opposite the organ windows, one of which is older than the present chapel and dates back to 1879. The other three stained glass windows presented in memory of WJ Litser, an old boy and Governor of the school for 25 years and thrice President of the OCA, depicting Bishop G.E.L Cotton, The Beryl Tobin and St Thomas, Apostle were installed in 1938.

 
The school choir has always been exceptional and has sung at two Viceregal weddings in New Delhi in 1938 and 1947, besides having sung over All India Radio. Even today the special carol service is famous. Morning assembly is held in the chapel daily and so the times gone by are bound in continuation with today and the times to come.