Following his diplomatic success in Spain, the Federalists chose Pinckney as John Adams's running mate in the 1796 presidential election. Under the rules then in place, the individual who won the most electoral votes became president, while the individual who won the second most electoral votes became vice president. Although Adams won the presidential election, Democratic-Republican candidate Thomas Jefferson won the second most electoral votes and won election as vice president. After the election, Pinckney served in the United States House of Representatives from 1797 to 1801. His brother, Charles Cotesworth Pinckney, was the Federalist vice presidential nominee in 1800 and the party's presidential nominee in 1804 and 1808. During the War of 1812, Pinckney was commissioned as a major general.