Bhupathi Mohan Sen had his early education in Rajshahi Collegiate School and Rajshahi College. After completing school education he took admission in Presidency College and passed his B.Sc. Examination in 1908, with triple Honours, first class in Mathematics, second class in Physics and second class in Chemistry. In 1910 he obtained the M.Sc. degree from Calcutta University occupying first position in the first class in Applied Mathematics. After completing his M.Sc. degree he went to Cambridge as a foundation scholar of King's College for the period 1911–1915. In 1912 he took up his M.A. degree of Cambridge University obtaining the distinction of being a Senior Wrangler with the mark of distinction in special subjects. In 1914 he won Smith's prize from Cambridge University for his very great academic distinction. He was the first Indian to win this prize.