McKee was elected as an Unconditional Unionist to the Thirty-ninth Congress (March 4, 1865 – March 3, 1867). He successfully contested as a Republican the election of John D. Young to the Fortieth Congress and served from June 22, 1868, to March 3, 1869.
He was not a candidate for renomination in 1868. He served as delegate to the Southern Loyalist Convention at Philadelphia in 1866. He worked as a pension agent in Louisville, Kentucky from 1869 to 1871. He resumed the practice of law. He died in Louisville, Kentucky on December 11, 1898. He was interred in Cave Hill Cemetery in Louisville.