On January 24, 2014, Gainer was appointed the eleventh Bishop of Harrisburg, Pennsylvania, by Pope Francis. He was installed on the following March 19 in the Cathedral of St. Patrick, Harrisburg.
Ban on female students in contact sports
On July 1, 2014, Gainer introduced a new policy prohibiting girls at Catholic schools in the Diocese of Harrisburg from participating in wrestling, tackle football, and tackle rugby whether or not they desire to compete in girls-only or co-ed matches. The policy goes on to require male wrestlers to forfeit matches against female opponents, but does not bar tackle football or rugby teams from playing against teams which may have a girl on their team. According to the policy, the ban applies to sports "...that involve substantial and potentially immodest physical contact".
Response to clergy sex abuse and grand jury investigation
In early 2016, a grand jury investigation, led by Pennsylvania Attorney GeneralJosh Shapiro, began an inquiry into sexual abuse by Catholic clergy in six Pennsylvania dioceses: Harrisburg, Allentown, Scranton, Pittsburgh, Greensburg, and Erie. The Diocese of Altoona-Johnstown and the Archdiocese of Philadelphia were not included, as they had been the subjects of earlier investigations. According to The Philadelphia Inquirer, in 2017 the Diocese of Harrisburg and the Diocese of Greensburg attempted to shut down the grand jury investigation. On July 27, 2018, the Pennsylvania Supreme Court ordered that a redacted copy of the grand jury report be released to the public; this release is anticipated to occur in early August 2018. On August 1, 2018, Bishop Gainer disclosed the names of 71 past and present clergy affiliated with the Diocese of Harrisburg who were accused of sexually abusing children. Among these 71, the majority are already deceased, and some were accused only after their deaths. Gainer explained the rationale for the release of this information: "While these men are not a risk to the public, I still felt compelled to release their names in an effort to confirm for those brave survivors... that we have heard their cries and taken them seriously." Gainer also stated that prior to 2002, some lawsuits had been settled using confidentiality clauses, and he was now releasing all victims from such confidentiality agreements. Immediately following the disclosure, Gainer announced that the name of every man who had served as a bishop in the Diocese of Harrisburg since 1947 would be removed from any building or room named in their honor, due to their failure to protect victims from abuse.
