Background: Craniovertebral junction (CVJ) anomalies involve mosaic interaction of multifaceted neurovascular and bony elements. Most of them present late in the course of illness usually as acute presentations following trivial trauma. Knowing subclinical autonomic dysfunction in such anomalies when managed medically can not only indicate progression but also provide en route to early intervention for better outcomes, especially in relatively asymptomatic patients. Materials and Methods: We conducted a 6-year longitudinal prospective study including 40 consecutive patients of CVJ anomalies with clinical, radiological, and heart rate variability (HRV) parameters and found their correlation in preoperative and follow-up period. Results: Twenty-eight patients were male and the rest were female. The mean age was 32 years with the least age being 8 years and maximum age being 75 years old. Mean Nurick's grade and Barthel's index were 1.8 and 83.75, respectively. 38% had severe-to-moderate compression. The mean follow-up was 17.4 months. Both sympathetic and parasympathetic oscillator HRV indices were significantly affected in the preoperative period ( P ≤ 0.001) with no association with Nurick's grade or degree of compression although there was association with grade of Barthel's index. Poincare plots showed “fan,” “complex,” or “torpedo” patterns in 36 patients. Forty patients had both preoperative and follow-up clinical grade whereas 22 patients HRV tests in the above periods. None of the HRV indices showed significant improvement at follow-up. Nonetheless both sympathetic and parasympathetic did improve at follow-up with sympathetic tone registering better scores. Poincare plots showed improvement toward “comet” patterns in all patients. Conclusion: HRV indices not only help in prognosticating but may also help in predicting outcomes.