The Tampa Bay Rays selected Lobstein in the second round of the 2008 Major League Baseball Draft. Lobstein was selected in the 2012 Rule 5 draft by the New York Mets, and traded that same day to the Detroit Tigers. The Tigers added Lobstein to their 40-man roster on November 20, 2013. On August 23, 2014, the Tigers promoted Lobstein to the major leagues before a doubleheader against the Minnesota Twins. Prior to being called up, Lobstein was 9–11 with a 4.07 ERA and a 1.479 WHIP in 26 games with the Triple-AToledo Mud Hens. Lobstein made his debut in the first game of the doubleheader, pitching innings, allowing three runs on four hits, while walking four, and striking out three. Lobstein made his first major league start on August 28, against the New York Yankees. He pitched six innings, allowing two runs, one earned, on four hits and one walk, while earning a no-decision. Following the game, Lobstein was optioned back to Triple-A Toledo. On September 2, Lobstein was recalled from Triple-A, and made his second major league start of the season that night against the Cleveland Indians. Lobstein pitched innings, allowing two runs on five hits, while walking three and striking out a career-high ten batters. On September 7, Lobstein pitched innings, allowing one run on four hits, while walking two and striking out three, to earn his first major league win over the San Francisco Giants. Lobstein opened the 2015 season in the Tigers rotation due to Justin Verlander not being able to start the season with a right triceps strain. Lobstein had a 3–5 record, with a 4.34 ERA and a 1.448 WHIP in eight starts before being placed on the disabled list with left shoulder soreness on May 24, 2015. During his rehab assignment, he pitched two starts for the Class-A AdvancedLakeland Flying Tigers and four for the Triple-A Toledo Mud Hens. He went 0–3 with a 5.68 ERA between the two stops. The Tigers activated Lobstein from the disabled list on September 3, 2015. During the 2015 season, Lobstein went 3–8 with a 5.94 ERA and a 1.586 WHIP in 13 outings, including 11 starts with the Tigers. He was designated for assignment by the Tigers on December 18, 2015.
Pittsburgh Pirates
On December 21, 2015, Lobstein was traded to the Pittsburgh Pirates in exchange for cash considerations. Through 14 games with the Pirates in 2016, Lobstein recorded a 3.96 ERA over 25 innings. He gave up 11 earned runs on 25 hits while walking 12 batters. On August 30, 2016, Lobstein was designated for assignment.
On August 31, 2016, Lobstein was traded to the Baltimore Orioles for minor league pitcher Zach Phillips. He was designated for assignment that same day when the Orioles acquired Drew Stubbs. He was sent outright to the Triple-A Norfolk Tides on September 3, where he pitched in one game before their season ended. He elected free agency on October 5.
On March 20, 2018, Lobstein signed with the Toros de Tijuana of the Mexican Baseball League. Lobstein finished out the Spring Tournament of the season, recording a 4-2 record and a 2.95 ERA across 11 starts.
Los Angeles Dodgers
On June 22, 2018, Lobstein signed a minor-league contract with the Los Angeles Dodgers. He was 4–7 with a 3.79 ERA across 14 starts for AA Tulsa and AAA Oklahoma City. Lobstein elected free agency on November 2, 2018.
