Background: With the emergence of human papillomavirus-based primary screening, the option of vaginal self-collected sample may overcome the barrier of speculum examination. Despite evidence of high acceptability of self-collection, there is need to evaluate the validity of such samples for HPV detection. This research aimed to determine the validity of self-collected vaginal samples for HPV detection among Nigerian women. Methods: A cross-sectional analytic study was conducted among 230 asymptomatic women, selected by multi-stage sampling method in Orhuwhorun community in Udu Local Government Area of Delta State between May to June 2021. Participants were instructed on self-collection (SC) of vaginal samples using Flobam female sample collection kit and a clinician-collected (CC) cervical sample was obtained using a similar swab. Paired specimens were tested for HPV genotyping using 21 HPV GenoArray Diagnostic kits. SPSS vs 25 was used for data analysis. Agreement between the two collection methods was calculated using concordance and discordance rates and Cohen's kappa statistic. A 2 by 2 contingency table was used to calculate sensitivity and specificity of both sampling methods. A p < 0.05 was considered statistically significant. Results: 230 women of mean age 41.08 years (SD ± 8.45) were enrolled and 228 paired SC and CC results were analyzed. Of the 228 samples, 44 (19.3%) and 48 (21.1%) had HPV on clinician-collected and self-collected samples respectively. The HPV detection concordance was 92.9% (95%CI: 89.7–96.3), Kappa value of 0.66 (p < 0. 001), showing substantial agreement. Sensitivity and specificity of SC compared to CC were 86.4% (95%CI: 76.2–96.5) and 94.6% (95%CI: 91.3–97.8) respectively. Odds ratio was 1.15 indicating SC is as good as CC for HPV detection. Conclusions: The excellent validity of SC support its use as an alternative form of HPV screening among Nigerian women hence the government should consider its introduction into the national cervical screening programme.