Whaley joined the team as assistant general manager in 2010 and was later hired as general manager in 2013 after Buddy Nix stepped down following that year's draft. In Whaley's four seasons as general manager, the team finished 30-34 and had just one winning season (2014).
The Bills also terminated the professional and amateur scouting departments, Pegula said at a press conference Sunday.
Whaley seemed to at least be on the hot seat, if not nearing the end of his tenure when he admitted he wasn't included in the conversations surrounding the firing of head coach Rex Ryan.
"The decision was made now because this is the end of the scouting year," Pegula said. "We ran a process and as a result of that process after the draft we made the decision."
"He put the whole thing together," Pegula said of Whaley's involvement with the 2017 draft.
NFL Network Insider Ian Rapoport reported the scouting community expected the move, adding new Bills head coach Sean McDermott had a heavy hand in Buffalo's draft-night trade.
In addition, Don Gregory, the Panthers' director of player personnel is considered a potential candidate for the vacancy as is Brett Veach, the Chiefs' co-director of player personnel, Rapoport reported. Buffalo has also received permission to interview Texans director of pro personnel Brian Gaine, NFL Network's Mike Garafolo reported.
McDermott will be consulted by ownership during the GM search, Pegula said.
"Sure, I will ask Sean questions," Pegula said. "We will use every resource available."
Whaley's draft tenure was marred by injuries to his lone two first round picks -- receiver Sammy Watkins and defensive end Shaq Lawson -- and later-round selections that failed to stick, as well as the albatross he immediately inherited and for which he was forced to find an alternative in E.J. Manuel. The Watkins selection became uglier after repeated struggles with foot issues, as well as the fact Whaley dealt away a 2015 first-round pick (and fourth-round selection) to move up to grab the wideout.
Whaley also had some painfully memorable meetings with the media (as few and far between as they came), going immediately on the defensive in one of his last press conferences as GM, which included a reporter saying "I'm actually trying to figure out what you (Whaley) do for a living" while questioning Whaley's nonexistent role in Ryan's firing.
While it's somewhat peculiar to see a personnel decision-maker fired just hours after the three most important roster construction days of the calendar, this isn't the first time a GM has left his post in Buffalo after completing a draft. Nix, whom Whaley replaced, stepped down from the position just weeks after the 2013 draft, in which Buffalo selected Manuel. The passer was at the center of one of the final decisions made with Whaley's input, resulting in the benching of Tyrod Taylor in what was classified as an injury-related "business decision" -- Taylor's contract would have become fully guaranteed at $30.75 million had he suffered an injury in the final week of the 2016 season -- and to see what the Bills had in Manuel.