Introduction This single-blind randomized trial was conducted to compare the treatment effect of lower limb (LL) exercises versus conventional lumbar extensor (LE) and lumbar stabilization (LS) exercises in recreational runners with chronic low back pain (cLBP), because there is currently no specific protocol for managing runners with cLBP. Methods Eighty-four recreational runners with cLBP were allocated to three exercise groups (LL, LE, LS) for an 8-wk intervention. Outcome measures included self-rated pain and running capability, LL strength, back muscle function, and running gait. Participants were assessed at preintervention, mid-intervention, and end-intervention; selected outcomes also followed up at 3 and 6 months. Generalized estimating equation was adopted to examine group-time interaction. Results The LL group improved 0.949 points per time point in Patient-Specific Functional Scale (P < 0.001), which was higher than the LE (B = -0.198, P = 0.001) and LS groups (B = -0.263, P < 0.001). All three groups improved on average 0.746 points per time point in Numeric Pain Rating Scale for running-induced pain (P < 0.001). Knee extension strength increased 0.260 Nmkg(-1) per time point (P < 0.001) in the LL group, which was higher than the LE (B = -0.220, P < 0.001) and LS groups (B = -0.206, P < 0.001). The LL group also showed a greater increase in running step length (2.464 cm per time point, P = 0.001) compared with LS group (B = -2.213, P = 0.013). All three groups improved similarly in back muscle function. Conclusion LL exercise therapy could be a new option for cLPB management given its superior effects in improving running capability, knee extension strength, and running gait.