During World War I, he enlisted in the Sixth Regiment, Missouri Infantry, on April 8, 1917.

He served as captain of Company G, One Hundred and Fortieth Infantry Regiment, Thirty-fifth Division, from August 4, 1917, to May 15, 1919.

Milligan was elected as a Democrat to the Sixty-sixth Congress to fill the vacancy caused by the resignation of Joshua W. Alexander and served from February 14, 1920, to March 3, 1921.

Milligan was elected to the Sixty-eighth and to the five succeeding Congresses (March 4, 1923 – January 3, 1935).

Jacob Milligan resumed the practice of law and served as president of Kansas City Police Board from 1949 to 1950.