John Jones Milligan (December 10, 1795 – April 20, 1875) was an American lawyer and politician from Wilmington, in New Castle County, Delaware.

He was a member of the Whig Party, and served as U.S. Representative from Delaware.

Having been defeated for reelection to a fifth term, he was appointed Associate Judge of the Delaware Superior Court on September 19, 1839, and served until September 16, 1864, when he retired.

Milligan is described in the Diaries of Edmund Canby as follows: "...(he)...is a beautiful speaker, his manner is fine, gestures good, matter well arranged, distinct and clear- certainly one of the most delightful speakers I have ever heard...Milligan would be a splendid speaker with practice...he has many happy hits and some beautiful classical illusions...He is, I am told, a fine classical scholar.

Representatives took office March 4 and have a two-year term.