He continued work as the state supreme court reporter and continued his private legal practice. He made a good living and attracted the attention of powerful politicians. President Ulysses S. Grant appointed him to defend the government in a suit by Lambdin Milligan, a lawyer who was a vocal opponent of the war. Federal officials arrested Milligan, who responded with a lawsuit that eventually reached the U.S. Supreme Court, which sided with Milligan in the famous case Ex parte Milligan (1866). The Supreme Court ruled that federal officials exceeded their lawful authority in arresting Milligan and hauling him before a military tribunal.

Because of the Court’s decision, Milligan’s case went back to a trial court for a jury hearing. Grant appointed Harrison to argue for the government before the jury. Harrison was an excellent attorney and he persuaded the jury to award Milligan only nominal damages—a total of five dollars.