After several terms in the state legislature, Eustis won election to the United States Congress in 1800, serving as a moderate Democratic-Republican. He briefly returned to state politics after losing reelection in 1804, and was chosen to be Secretary of War in 1809 by President James Madison. Due in part to his inexperience at managing the army and a lack of preparedness, the military failures in the early months of the War of 1812 were laid on his shoulders, leading to his resignation.