Although born in Wyoming, Nickerson grew up in Oregon City, Oregon, and played prep baseball there. He lettered 3 times in baseball and held a successful career at Oregon City. He graduated from Oregon City High School in 2003. At a local rally in Oregon City on July 7, 2006, Nickerson was honored with the keys to the city by Mayor Alice Norris, who also proclaimed July 7 as "Jonah Nickerson Day".
College career
A 6'1", 190 lb right-hander, Nickerson posted a record of 13–4 during the 2006 season, including three games (two victories and one no-decision) during the College World Series; one of them, a victory against Rice University which qualified the Beavers for the Finals, came on two days' rest. His earned run average (ERA) for the regular season was 2.50. He was named an All-American in both 2005 and 2006.