Background: Countries with high human papillomavirus (HPV) vaccination rates have achieved this success largely through school-based vaccination. Using school-based health centers (SBHCs) in the United States, where HPV vaccine remains underutilized, could improve uptake. In this mixed-methods study, we examined acceptability, facilitators, and barriers of HPV vaccination visits at SBHCs from the perspectives of adolescents and parents. Methods: We conducted qualitative interviews and structured surveys with adolescents and parents recruited from an urban, hospital-based clinic. Interviews with parents (N = 20) and adolescents (N = 20) were audio-recorded and transcribed for analysis using an iterative thematic approach. Quantitative measures for a survey administered to parents (N = 131) were derived from the qualitative findings. Survey results were analyzed by chi-square tests. Results: Many participants expressed favorable opinions of HPV vaccination at SBHCs in qualitative interviews. Facilitators included convenience, ease of scheduling, and not missing work or school. However, barriers were noted including concerns about obtaining care outside the medical home, fragmentation of medical records, and negative perceptions about SBHCs. Quantitative findings revealed that a higher proportion of parents with experience using SBHCs were willing to use a middle school (59.5%) or high school (80.5%) SBHC for HPV vaccinations compared with those who had not used SBHCs (p < 0.05 for both comparisons). Conclusions: HPV vaccination visits at SBHCs were acceptable, and SBHC users expressed more favorable attitudes. Barriers to HPV vaccination at SBHCs can be addressed through more education about SBHCs' role, and improvement of systems to coordinate care.