Branyan hit two home runs on August 29 against the Arizona Diamondbacks. The first home run in the seventh inning against Brandon Webb went an estimated 422 feet, and the second came in the ninth inning against Jorge Julio went an estimated 456 feet. Branyan hit his fifth home run as a member of the Padres on September 24, against the Pittsburgh Pirates. When recorded, it was the longest in Petco Park history, going an estimated 453 feet. He hit .292 for the Padres with 6 home runs, 9 RBIs, 14 runs scored and 15 walks. He compiled a .416 on-base percentage while slugging .556. He started at third base in 26 of San Diego's final 33 games and committed only 3 errors in 45 total chances. His 18 home runs overall in 2006 were the most he hit in a single season since 2002. At the end of the season it was speculated that Branyan would have a sure spot on the roster out of spring training. On October 30, Branyan's $1,000,000 option was picked up by the Padres.