If i have protected sex and am on birth control could i be pregnant?

All forms of BC have a failure rate, some more than others. You did not mention the form of BC or protection you are using so it is hard to be specific. Some women on BC begin to skip menses or even stop. Some normal women will skip a cycle occasionally.

If you take your birth control regularly, and he wore a condom throughout the intercourse, you are are not pregnant. Get HPV vaccine. Safe sex: https://www.hopkinsmedicine.org/health/wellness-and-prevention/safer-sex-guidelines