Vargas transferred to California State University, Long Beach to play for the Long Beach State 49ers for his junior year. At Long Beach, he learned to keep his top half aligned with his lower half over the rubber and not drift toward the plate as he twisted through his delivery. The tweak allowed Vargas to repeat his mechanics and keep his arm higher, which in turn increased the velocity on his fastball and improved the break on his curveball. The new work ethic paid off, and in Vargas went 7–4 with a 4.14 ERA in 18 games on the mound, while hitting .354 with 14 doubles and five home runs as the team's designated hitter.