Bishop of Newcastle Greg Thompson said he was stepping down from his position for health reasons.
While presenting evidence to the Royal Commission into Institutional Responses to Child Sexual Abuse in November, Bishop Greg claimed he was also abused as a young man by senior church clerics.
He said that after working to expose the culture of abuse cover ups, some parishioners had placed screws in his staff members' tyres and that he was ostracised by members of the congregation.
The announcement of his resignation comes the day before Bishop Greg is due to give more evidence at the Royal Commission.
"When I started this journey to right the wrongs of child abuse in the diocese I didn't expect to be in this position, nor did I expect to uncover systemic practices that have enabled the horrendous crimes against children," Bishop Greg said in a statement released to the media on Thursday.
"The decision to resign was not an easy one, it weighed heavily on my heart. However, I must place the wellbeing of my family and my health above my job."
Bishop Greg is the second senior member of the Newcastle diocese to resign over the issue of the handling of child sexual abuse in recent months.
The diocese business manager John Cleary stepped down from his role on 27 February.
In November, Bishop Greg told the Commission said that the Anglican "house is burning" and that the Australian Anglican church must take action against systemic child sexual abuse.
Bishop Greg will formally end his tenure on 31 May.
The Assistant Bishop of Newcastle, Peter Stuart expressed his sadness over Bishop Greg's decision.
"In his short time as our Bishop, he has been the catalyst for deep cultural change around the protection of children and the support of victims of abuse. He called us to face our past and in doing so shape a healthy future. This will be his enduring legacy," Bishop Stuart said.
The Royal Commission into Institutional Responses to Child Sexual Abuse is a royal commission established in 2013 by the Australian government to investigate the history of abuse in educational and religious institutions.