Background The aim of this study was to compare health-related quality of life (HRQoL) and disability and fear of movement in patients with non-specific chronic neck pain (NSCNP) associated with dizziness with respect to patients with isolated NSCNP in primary care settings. Methods A cross-sectional study was carried out in a primary care center. A total of 120 patients were divided into two groups and analyzed in this study. One group of patients reported dizziness combined with NSCNP (n = 60), and the other reported no dizziness with their NSCNP (n = 60). Patient-reported outcome measurements were HRQoL (primary outcome) and disability and kinesiophobia (secondary outcomes) assessed by the EuroQoL Five Dimensions and Five Levels (EQ-5D-5L), neck disability index (NDI) and Tampa Scale of Kinesiophobia (TSK-11), respectively. Results Statistically significant differences (P < 0.05) for a 95% confidence interval (CI) with a large effect size (Cohen d) were found between both groups with greater values of disability (mean difference = 6.30 points; 95% CI [3.84–8.75]; d = 0.94) and kinesiophobia (mean difference = 8.36 points; 95% CI [6.07–10.65]; d = 1.33), and an impairment of HRQoL (mean difference = 16.16 points; 95% CI [11.09–21.23]; d = 1.16), for patients with NSCNP associated with dizziness with respect to patients with isolated NSCNP. Conclusions Patients with NSCNP in conjunction with dizziness present higher HRQoL impairment and higher disability and kinesiophobia compared to patients with isolated NSCNP.