Pat Conroy, the House chaplain, to rescind his resignation, following a week's worth of lawmakers from both parties questioning Ryan's request that Conroy step down.
"My original decision was made in what I believed to be the best interest of this institution", Ryan said.
During a conference earlier this week, Ryan insisted his decision to oust Conroy wasn't political, but performance-based, "and a number of our members felt like the pastoral services were not being adequately served, or offered".
House Republicans say that Ryan assured them the prayer wasn't a factor, but rather that some had approached him with concern "that their pastoral needs weren't being met", in the words of Rep. Mark Amodei, R-NV.
Lawmakers, including some Republicans, had urged Ryan to keep Conroy on as the House chaplain.
Conroy's resignation and subsequent public feuding with Ryan has ballooned into scandal.
Conroy then insisted that not only would he not be resigning, but also that if Ryan in fact wanted him removed from his position, he would have to terminate him.
The Jesuit priest said that he had never been disciplined, and had received zero complaints about his ministry during his almost seven years as House chaplain, but felt as though he was being forced into resigning by Ryan.
"It's going to be more trouble than it's worth", Wilson said, and will now be hard for Ryan to "extricate himself gracefully".
Last November, Conroy prayed for lawmakers to make sure that "there are not winners and losers under new tax laws, but benefits balanced and shared by all Americans".
In his letter on Thursday, Conroy suggested his faith may have played a role.
"This is not the reason that Mr. Burks gave me when asking for my 'resignation, '" the reverend wrote.
"I inquired as to whether or not it was 'for cause, ' and Mr. Burks mentioned something dismissively like 'maybe it's time that we had a Chaplain that wasn't a Catholic, '" Conroy wrote to Ryan in a letter that was also sent to House Minority Leader Nancy Pelosi, D-Calif.
"In retracting my resignation, I wish to do just that", he wrote.
Ryan "didn't say this as bluntly but the reason for the change is that many of us like Father Conroy but we feel like he didn't do anything", another unnamed Republican told CNN.
A congressional aide for Ryan told the Times that no specific prayer was the cause of the decision.