Purpose: To investigate differences between rating of perceived exertion (RPE) and percentage one-repetition maximum (1RM) load assignment in resistance-trained males (19–35 years) performing protocols with matched sets and repetitions differentiated by load-assignment.Methods: Participants performed squats then bench press 3x/weeks in a daily undulating format over 8-weeks. Participants were counterbalanced by pre-test 1RM then assigned to percentage 1RM (1RMG, n = 11); load-assignment via percentage 1RMs, or RPE groups (RPEG, n = 10); participant-selected loads to reach target RPE ranges. Ultrasonography determined pre and post-test pectoralis (PMT), and vastus lateralis muscle thickness at 50 (VLMT50) and 70% (VLMT70) femur-length.Results: Bench press (1RMG +9.64 ± 5.36; RPEG + 10.70 ± 3.30 kg), squat (1RMG + 13.91 ± 5.89; RPEG + 17.05 ± 5.44 kg) and their combined-total 1RMs (1RMG + 23.55 ± 10.38; RPEG + 27.75 ± 7.94 kg) increased (p < 0.05) in both groups as did PMT (1RMG + 1.59 ± 1.33; RPEG +1.90 ± 1.91 mm), VLMT50 (1RMG +2.13 ± 1.95; RPEG + 1.85 ± 1.97 mm) and VLMT70 (1RMG + 2.40 ± 2.22; RPEG + 2.31 ± 2.27 mm). Between-group differences were non-significant (p > 0.05). Magnitude-based inferences revealed 79, 57, and 72% chances of mean small effect size (ES) advantages for squat; ES 90% confidence limits (CL) = 0.50 ± 0.63, bench press; ES 90% CL = 0.28 ± 0.73, and combined-total; ES 90% CL = 0.48 ± 0.68 respectively, in RPEG. There were 4, 14, and 6% chances 1RMG had a strength advantage of the same magnitude, and 18, 29, and 22% chances, respectively of trivial differences between groups.Conclusions: Both loading-types are effective. However, RPE-based loading may provide a small 1RM strength advantage in a majority of individuals.