Urine-based self-sampling approaches can simplify cervical screening programs whilst increasing response. This study reports on the performance of Abbott Alinity m HR HPV on urine, self-collected at home using a new generation first-void urination device that is suitable for postal delivery (Novosanis Colli-Pee Small Volumes). First-void urine and paired cervical samples from 297 females attending colposcopy (age 25–65, NCT04530201) were analysed for the presence of Human Papillomavirus (HPV) DNA. Cervical disease was confirmed by colposcopy and/or histology. HPV testing on first-void urine was less sensitive for high-grade cervical intraepithelial neoplasia (CIN2 +; ratio 0.91; 95% CI: 0.83–0.99), though equally specific (< CIN2; ratio 1.04; 95% CI: 0.92–1.19) compared to cervical samples at the manufacturer established cut-off for cervical samples. Adjusting the cut-off for first-void urine improved sensitivity for CIN2+ (ratio 0.96; 95% CI: 0.90–1.03), whilst maintaining equal specificity compared to cervical samples (ratio 1.00; 95% CI: 0.88–1.14). Cohen's kappa agreements of HPV outcomes between sample pairs were good to excellent at both cut-offs (range: 0.64–0.85). Using the HPV test's adjusted cutoff for first-void urine, no difference in clinical sensitivity or specificity was observed between first-void urine and cervical samples. These data highlight the importance of evaluating self-sample-specific cut-offs for HPV assays, previously validated on cervical samples.