Female runners have a two-fold risk of sustaining certain running-related injuries as compared to their male counterparts. Thus, a comprehensive understanding of the sex-related differences in running kinematics is necessary. However, previous studies have either used discrete time point variables and inferential statistics and/or relatively small subject numbers. Therefore, the first purpose of this study was to use a principal component analysis (PCA) method along with a support vector machine (SVM) classifier to examine the differences in running gait kinematics between female and male runners across a large sample of the running population as well as between two age-specific sub-groups. Bilateral 3-dimensional lower extremity gait kinematic data were collected during treadmill running. Data were analysed on the complete sample (n = 483: female 263, male 220), a younger subject group (n = 56), and an older subject group (n = 51). The PC scores were first sorted by the percentage of variance explained and we also employed a novel approach wherein PCs were sorted based on between-gender statistical effect sizes. An SVM was used to determine if the sex and age conditions were separable and classifiable based on the PCA. Forty PCs explained 84.74% of the variance in the data and an SVM classification accuracy of 86.34% was found between female and male runners. Classification accuracies between genders for younger subjects were higher than a subgroup of older runners. The observed interactions between age and gender suggest these factors must be considered together when trying to create homogenous sub-groups for research purposes.