Introduction: Laser acupuncture (LA) is a medically approved treatment for chronic pain, especially fibromyalgia. It is widely known that all pain is related to autonomic modulation, which may influence heart rate variability (HRV). There are robust studies in the literature on the effect of LA with continuous frequency on musculoskeletal pain and autonomic modulation. However, little is known about the effect of pulsed frequency on fibromyalgia. Therefore, this study aimed to evaluate whether an individualized intervention protocol applying pulsed LA would provide benefits related to pain symptoms and cardiac autonomic modulation in patients with fibromyalgia. Methods: In this pilot randomized clinical controlled trial, the sample consisted of women with fibromyalgia between the ages of 40 and 80, randomized into two groups: a control group (CG; n=10) and an experimental group (EG; n=10). EG received the intervention twice per week for 3 weeks. Statistical analysis was conducted by delta (difference between post-intervention and pre-intervention) and the Shapiro-Wilk test (normality). For comparison between the groups, the Mann-Whitney test was used. Results: The results showed a significant reduction in pain intensity as reported via the pain numerical scale (PNS; P=0.00), generalized pain index (GPI; P=0.00), and symptom severity scale (SSS; P=0.00). There was no significant difference in any HRV variable (P>0.05). Conclusion: Pulsed LA, when applied in an individualized protocol, can reduce pain intensity, as reported on the PNS, GPI, and SSS. However, no therapeutic effect was observed for HRV.