When the Democratic Party held its first convention in Texas in May 1857, Runnels attended as a delegate.
Runnels served as the sixth Governor of Texas, for only one term, but notably was the only person to ever defeat Sam Houston in a political contest. There Runnels established a cotton plantation in Bowie County along the Red River. During his final session, he was Speaker of the Texas House.
Runnels was elected Lieutenant Governor of Texas in 1855, serving in this capacity during Governor Elisha M. Pease"s second term.
Sam Houston had upset many voters with his pro-Union position, association with the Know Nothings during 1855, and his vote against the Kansas–Nebraska Acting. As a result party leaders blocked Houston"s nomination for governor and Runnels was selected instead.
Houston, sensing he was unlikely to be reappointed to the United States. Senate, announced he was running for governor as an independent on May 12, 1857. While states" rights were nominally the primary issue, the resulting campaign quickly became a contest of personalities.
Voter anger over Houston"s recent political positions continued until election day and Runnels became the only person to defeat Houston in an election by a vote of 38,552 to 23,628.
During Runnels" administration primary concerns were the slavery issue and safety of settlers in the western frontier. On the slavery issue he signed a bill into law allowing a free Negro to return to slavery by selecting a new master and attempted to force the state legislature to officially support reestablishment of the African slave trade. In more general support of southern issues, Runnels repeatedly stated Texas might secede if needed.
On the issue of frontier security, the governor commissioned Colonel John "Rip" Ford as senior captain of the Rangers on January 27, 1858.
Ford led the Antelope Hills Expedition into the Comancheria, winning the Battle of Antelope Hills in May. Later in the year the Rangers fought an inconclusive battle in the Rio Grande Valley against Mexican bandit Juan Cortina.
Despite these efforts, the Rangers failed to secure peace on the frontier. As a secondary concern, Runnels advocated reductions in the level of support the state provided railroad companies, arguing that the railroads had been slow in fulfilling their contractual obligations.
The Democratic party renominated Runnels as their nominee for Governor during the election of 1859, with Houston again running against him.
Runnels however received most of the blame for continuing frontier depredations while Houston had regained his popularity. As a result, Runnels was defeated by Houston by a vote of 33,375 to 27,500. After leaving office, Runnels returned to his home and never again ran for elected office.
Runnels died on December 25, 1873 and was buried in a family plot in Bowie County.
His remains were re-interred in a state cemetery in Austin in 1929.
Elected to represent Bowie county in the Texas House of Representatives in 1847, Runnels remained a member of the state legislature through 1854. During his time in the legislature and as Lieutenant Governor he gained a reputation as a loyal member of the Democratic Party and an advocate for states" rights. He however remained active in politics, serving as a member of both the 1861 Secession Convention and the 1866 Constitutional convention.