In 1872, Pratt was elected as a Republican to represent Iowa's 4th congressional district in the 43rd United States Congress. He was re-elected two years later, and served in the 44th United States Congress. He was not a candidate for renomination in 1876. He served in Congress from March 4, 1873 to March 3, 1877.
Returning to Iowa, he served as president of the 1877 Republican State Convention. After studying for the ministry, he was ordained and entered the ministry of the Methodist Episcopal Church in October 1877. He continued his ministerial duties until retired on account of age in October 1918.