To compare lower limb joint angle variability between functional ankle instability (FAI) and healthy controls (CONs) at different running speeds using linear and nonlinear methods. Fifteen males with right-side FAI and fifteen matched CONs ran on a treadmill at self-selected, 20% faster, and 20% slower speeds. From 25 gait cycles, the mean coefficient of variation (CV), Sample Entropy (SampEn), and largest Lyapunov Exponent (LyE) of hip, knee, and ankle angles were computed. A two-way (two groups × three speeds) mixed-design ANOVA was applied (α = 0.05). No significant interaction effects were observed. No significant differences were observed in the CV. SampEn showed group effects: FAI had lower values in hip horizontal, knee sagittal/coronal, and ankle coronal planes, but higher in the hip sagittal plane. Speed effects showed greater SampEn in the ankle sagittal and lower in the hip coronal plane at slow speed. LyE was reduced in FAI for hip, knee, and ankle sagittal planes. Speed effects indicated higher LyE in the knee sagittal and lower in the hip coronal plane at slow speed. FAI showed reduced variability, particularly in the sagittal plane, reflecting rigid control. Slower speeds increased ankle and knee sagittal variability but decreased hip coronal variability.