He received his episcopal consecration on February 22, 2003, from Archbishop Thomas Kelly, with Bishops Edward Cullen and Joseph Kurtz serving as co-consecrators.

[5] In 2004, Gainer urged Catholic politicians who supported abortion rights for women to refrain from receiving communion.

[10] On April 25, 2023, Pope Francis accepted Gainer's resignation as he reached the canonical mandatory retirement age of 75.

[12] According to Gainer's policy, the ban applies to any women's sports "...that involve substantial and potentially immodest physical contact".

On August 1, 2018, Gainer disclosed the names of 71 past and present clergy affiliated with the Diocese of Harrisburg who were credibly accused of sexually abusing children.

[17]Immediately following the release of the list, Gainer announced removal of the names of all the bishops of Harrisburg since 1947 from buildings or rooms in diocesan facilities.