Each year, 50% of runners suffer from injuries. Consequently, more studies are being published about running biomechanics; these studies identify factors that can help prevent injuries. Scientific evidence suggests that recreational runners should use personalized biomechanical training plans, not only to improve their performance, but also to prevent injuries caused by the inability of amateur athletes to tolerate increased loads, and/or because of poor form. This study provides an overview of the different normative patterns of lower limb muscle activation and articular ranges of the pelvis during running, at self-selected speeds, in men and women. Methods: 38 healthy runners aged 18 to 49 years were included in this work. We examined eight muscles by applying two wearable superficial electromyography sensors and an inertial sensor for three-dimensional (3D) pelvis kinematics. Results: the largest differences were obtained for gluteus maximus activation in the first double float phase (p = 0.013) and second stance phase (p = 0.003), as well as in the gluteus medius in the second stance phase (p = 0.028). In both cases, the activation distribution was more homogeneous in men and presented significantly lower values than those obtained for women. In addition, there was a significantly higher percentage of total vastus medialis activation in women throughout the running cycle with the median (25th–75th percentile) for women being 12.50% (9.25–14) and 10% (9–12) for men. Women also had a greater range of pelvis rotation during running at self-selected speeds (p = 0.011). Conclusions: understanding the differences between men and women, in terms of muscle activation and pelvic kinematic values, could be especially useful to allow health professionals detect athletes who may be at risk of injury.