Fourteen randomized controlled trials, including 988 patients with joint pain from osteoarthritis, total knee replacement, adhesive capsulitis, and rheumatoid arthritis, were included in this systematic review and meta-analysis comparing intra-articular botulinum toxin type A (BoNT-A) with other treatments (saline, corticosteroids, hyaluronate, physical therapy, or usual care). Pooled outcomes of interest included pain intensity, activity limitations, and adverse events across short-term (<3 months), intermediate-term (3-6 months), and long-term (>6 months) follow-up periods. The pooled results showed that intra-articular BoNT-A had a significant reduction in pain and activity limitations in the short term for small to medium-sized joints (shoulder and base-of-thumb), but not for large joints (knee and ankle), and no significant differences were sustained in the intermediate or long term. Adverse events were generally minor and comparable between treatment groups. The main findings suggest that intra-articular BoNT-A may offer short-term pain relief in small and medium-sized joints, but its role in larger joints is limited.