Willis was elected as a Democrat to the Forty-fourth and Forty-fifth Congresses (March 4, 1875 – March 3, 1879). He served as chairman of the Committee on Expenditures in the Department of the Navy (Forty-fifth Congress). He was an unsuccessful candidate for reelection in 1878 to the Forty-sixth Congress. He engaged in the practice of law and also in the real estate business. He married Lillie Evelyn Macauley, daughter of William Macauley and Mary S. Underhill, and had three children: Kate T. Willis, Portia Willis and Benjamin A. Willis Jr. He died in New York City on October 14, 1886. He was interred in Friends Cemetery, Westbury, Long Island. He was reinterred in Woodlawn Cemetery.