This study aimed to identify mothers’ preferences and willingness-to-pay (WTP) for human papillomavirus (HPV) vaccines (in this case, bivalent and quadrivalent) in Iran. We used a discrete choice experiment (DCE) method to present mothers with choices between two hypothetical profiles of vaccines, described by combinations of five attributes, each with two or three levels. We analyzed the DCE results using conditional logistic regression and measured WTP estimates for each attribute. Our response rate was 53.96%, while the completion rate for questioner was 93.57%. We identified protection against cervical cancer, protection against genital warts, protection duration, serious side effects, and cost to influence mothers’ preferences for HPV vaccination. The relative importance for serious side effects was the highest among all attributes. Mothers’ WTP for bivalent and quadrivalent HPV vaccines was in US $ −432 (US $1 = IRR 42,000) and US $ 380, respectively. Quadrivalent vaccination could be the most suitable candidate for implementing the national immunization schedule. The reason is that mothers express more WTP for the quadrivalent vaccine than bivalent due to its protection against genital warts.