BackgroundFlight related low back pain (LBP) among helicopter pilots is frequent and may influence flight performance. Prolonged confined sitting during flights seems to weaken lumbar trunk (LT) muscles with associated secondary transient pain. Aim of the study was to investigate if structured training could improve muscular function and thus improve LBP related to flying.Methods39 helicopter pilots (35 men and 4 women), who reported flying related LBP on at least 1 of 3 missions last month, were allocated to two training programs over a 3-month period. Program A consisted of 10 exercises recommended for general LBP. Program B consisted of 4 exercises designed specifically to improve LT muscular endurance. The pilots were examined before and after the training using questionnaires for pain, function, quality of health and tests of LT muscular endurance as well as ultrasound measurements of the contractility of the lumbar multifidus muscle (LMM).ResultsApproximately half of the participants performed the training per-protocol. Participants in this subset group had comparable baseline characteristics as the total study sample. Pre and post analysis of all pilots included, showed participants had marked improvement in endurance and contractility of the LMM following training. Similarly, participants had improvement in function and quality of health. Participants in program B had significant improvement in pain, function and quality of health.ConclusionsThis study indicates that participants who performed a three months exercise program had improved muscle endurance at the end of the program. The helicopter pilots also experienced improved function and quality of health.Trial registrationIdentifier: NCT01788111 Registration date; February 5th, 2013, verified April 2016.Electronic supplementary materialThe online version of this article (doi:10.1186/s12891-017-1631-0) contains supplementary material, which is available to authorized users.