Rev Graham Sawyer from Briercliffe near Burnley was named a recipient of the accolade by the National Secular Society (NSS) after years spent trying to expose abuse within the Church.
He won the prize along with a survivor of clergy abuse, Phil Johnson, who founded the Minister and Clergy Sexual Abuse Survivors group.
Rev Sawyer, who leads St James Church in Briercliffe, was quoted by the Independent as saying: "When religious leaders are given secular power or one particular religion, let alone one group in one religion, is given a position of privilege by the state, we all too often see an abuse of power.
"Perhaps an example of this is the way that the established Church of England has treated victims of sexual abuse perpetrated by its leaders over so many years."
According to the NSS, the pair was nominated for the award "for their courageous campaigning work over many years to expose the institutional abuse of children and vulnerable adults in the Church of England in the face of institutional hostility".
NSS chief executive Stephen Evans was quoted by the Independent as saying: "We hope their work will cause those in positions of power to reflect on the damage done by excessive deference to religious authority.
"The Church of England must be held to account for its cover-up of abuse, including through independent oversight of its safeguarding policies."
A Church of England spokeswoman told the newspaper: "Phil Johnson is an invaluable voice on behalf of survivors with ongoing safeguarding work in the Church of England.
"As was demonstrated at the three-week IICSA hearings which have just finished, the church has made appalling mistakes and is absolutely committed to becoming a safer place for all and will continue to work with, and support survivors, to improve our responses to those who are at risk of being, or have been abused, as children or as adults."
Earlier this week, Archbishop of Canterbury Most Rev Justin Welby told the Independent Inquiry into Child Sexual Abuse how "ashamed" he was of the Church in the wake of the probe into how its leaders handled abuse allegations.
The Secularist of the Year has been described by the NSS as "an opportunity to celebrate the outstanding groups and inspiring individuals advancing secularism and related human rights", and the winner is awarded £5,000.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.