Background: Stand-up paddle boarding (SUP) is a rapidly growing global aquatic sport, with increasing popularity among participants within recreation, competition and rehabilitation. To date, few scientific studies have focused on SUP. Further, there is no research examining the biomechanics of the SUP paddle stroke. The purpose of this study was to investigate whether variations in kinematics existed among experienced and inexperienced SUP participants using three-dimensional motion analysis. This data could be of significance to participants, researchers, coaches and health practitioners to improve performance and inform injury minimization strategies. Methods: A cross-sectional observational design study was performed with seven experienced and 19 inexperienced paddlers whereby whole-body kinematic data were acquired using a six-camera Vicon motion capture system. Participants paddled on a SUP ergometer while three-dimensional range of motion (ROM) and peak joint angles were calculated for the shoulders, elbows, hips and trunk. Mann-Whitney U tests were conducted on the non-normally distributed data to evaluate differences between level of expertise. Results: Significant differences in joint kinematics were found between experienced and inexperienced participants, with inexperienced participants using greater overall shoulder ROM (78.9° ± 24.9° vs 56.6° ± 17.3°, p = 0.010) and less hip ROM than the experienced participants (50.0° ± 18.5° vs 66.4° ± 11.8°, p = 0.035). Experienced participants demonstrated increased shoulder motion at the end of the paddle stoke compared to the inexperienced participants (74.9° ± 16.3° vs 35.2° ± 28.5°, p = 0.001 minimum shoulder flexion) and more extension at the elbow (6.0° ± 9.2° minimum elbow flexion vs 24.8° ± 13.5°, p = 0.000) than the inexperienced participants. Discussion: The results of this study indicate several significant kinematic differences between the experienced and inexperienced SUP participants. These variations in technique were noted in the shoulder, elbow and hip and are evident in other aquatic paddling sports where injury rates are higher in these joints. These finding may be valuable for coaches, therapists and participants needing to maximize performance and minimize injury risk during participation in SUP.