On January 28, 2009, Runyan had microfacture surgery on his right knee. In February 2009, Runyan's contract expired with the team. He worked out for the Eagles on September 10, but did not sign a contract. He was signed by the San Diego Chargers, playing in five games before retiring.
In November 2009, published reports indicated Runyan was interested in running for Congress. On November 24, 2009, Runyan announced his congressional bid to challenge one-term Democratic incumbent John Adler for New Jersey's 3rd congressional district, which included parts of Burlington, Camden and Ocean Counties. Libertarian nominee Russ Conger and Your Country Again nominee Lawrence J. Donahue were also running. Even though he now played for the Chargers, he maintained a home in Mount Laurel, across the Delaware River from Philadelphia. On March 7, 2010, the Ocean County Republicans endorsed Runyan. On June 8, Runyan won the Republican nomination. On November 2, 2010, Runyan defeated Adler 50%–47%, becoming the first challenger to unseat an incumbent New Jersey Congressman since Rush Holt in 1998. He lost the Burlington and Camden portions of the district, but carried solidly Republican Ocean County by nearly 20,000 votes, far exceeding his overall winning margin of over 6,000 votes. Runyan is the fourth former NFL player to be elected to Congress, after Jack Kemp, Steve Largent, and Heath Shuler.