The protests and social media discussions have led some to ask if this is Nigeria's #MeToo moment.
In a video, that has been circulating on Twitter, the woman said the first incident happened at her father's house early one morning. The second incident happened on a secluded road. She gave detailed accounts of both attacks.
In a statement on Instagram, the pastor has said: "I have never in my life raped anybody even as an unbeliever and I am absolutely innocent of this."
Sunday's protests took place outside different branches of the pastor's church as people held placards saying: "Thou shall not rape."
Police and other security operatives protected the church in the capital, Abuja, and elsewhere congregants formed a ring around the church buildings stopping the protesters from entering.
On social media, people are sharing their experiences of alleged sexual assault at the hands of religious leaders, school teachers, housemaids, parents and neighbours.
They're using hashtags #MeToo, #ChurchToo and #SayNoToRape in what appears to be a shift in attitudes, with younger people feeling able to speak out about what's happened to them.
Of course, this is a discussion on social media, but Sunday's protests show that it is moving into the real world.
Nigeria has a huge Pentecostal Christian population, with some pastors often accused of extravagant lifestyles and flamboyance. Most of them have an overbearing influence on their followers.
People are now waiting to see what will be done in a country where rape is a criminal offence, but very few convictions have been obtained in court.