To analyze the effects on pain and disability recovery after a whiplash of a guided neck-specific exercise (NSE) therapy, compared to a different or an unguided NSE therapy. A literature search was conducted from inception to May 31, 2023, in three electronic databases: PubMed, ScienceDirect, and Web of Science. Eleven randomized controlled trials were included. Meta-analyses were performed with Review Manager software. The standardized mean difference (SMD) with a 95% confidence interval (CI) was used to measure the effect sizes and only short-term time points were considered. Not all studies reported a significant decrease of pain and disability in the NSE group compared to controls. However, meta-analyses demonstrated a significantly greater decrease in neck pain (SMD: -0.25; 95% CI: [-0.38, -0.12]; p = 0.0002) and neck-disability index (SMD: -0.35; 95% CI: [-0.54, -0.15]; p = 0.0005) in the NSE group. In addition to the benefits that a guided NSE therapy has on motivation and program adherence, it provides greater benefits in pain and disability than a different or unguided NSE therapy. Positive results are observed primarily with intervention periods of more than six weeks and at least two sessions per week.