Dynamic knee valgus (DKV) is a frontal plane knee kinematic alteration that has been associated with patellofemoral pain (PFP) in female runners. DKV is commonly assessed in clinical practice by measuring frontal plane knee projection angle (FPPA) during squat tests. However, it remains unclear whether the DKV observed in these tests is similar to or correlates with that observed during running in female runners. The aims of this cross-sectional study were to correlate and compare DKV, by measuring FPPA values, in a lateral step-down (LSD) squat test and running in female runners with and without PFP. A two-dimensional (2D) video analysis of the LSD test and running was carried out for 21 asymptomatic female runners and 17 PFP female runners in order to determine FPPA values. A Pearson correlation test and a factorial ANOVA with Bonferroni post hoc correction were used for statistical analysis. The FPPAs recorded in the LSD test were significantly higher than those recorded during running in the asymptomatic (16.32° ± 5.38 vs. 4.02° ± 3.26, p < 0.01) and PFP groups (17.54° ± 7.25 vs. 4.64° ± 3.62, p < 0.01). No significant differences were found in FPPA values between asymptomatic and PFP runners during the LSD test (16.32° ± 5.38 vs. 17.54° ± 7.25, p = 0.55) and running (4.02° ± 3.26 vs. 4.64° ± 3.62, p = 0.58). There was a small (r < 0.3) and non-significant (p > 0.05) correlation in FPPAs between the LSD test and running in both groups. According to our results, DKV was not similar during the LSD test and running, and there was no significant correlation in FPPA values between the LSD test and running in both groups. Therefore, clinicians and therapists should be aware of these findings when using the LSD test in clinical practice to evaluate DKV in female runners with or without PFP.