The Bills lost their first three games of the season, all by six points or less, and looked to be headed for a losing season. After a bye in Week Four, quarterback Rob Johnson finally won his first game with Buffalo, holding on for a 26–20 win over San Francisco in Week Five. Flutie started the next eleven games, winning nine of them. The Bills had a playoff spot locked up by the final game of the season, which Johnson started and won.
The Bills played the Dolphins in the Wild Card round of the 1998 AFC Playoffs, where wide receiverEric Moulds would set the NFL playoff record for receiving yards, with 240. The Bills would end up losing the game 17–24, as Dolphins lineman Trace Armstrong sacked Flutie on Buffalo's last drive, forcing him to fumble, and icing the game for Miami.
The Bills, looking to upgrade the quarterback position, signed Rob Johnson, who had played for Jacksonville in 1997, and improved his stock with a win in relief of Jaguars quarterback Mark Brunell. Bills general manager John Butler traded away the Bills' first- and fourth-round picks to Jacksonville for the rights to Johnson.
The opening game for 1998 constituted the first time since 1985 that the Bills played the San Diego Chargers. The reason for this is that before the admission of the Texans in 2002, NFL scheduling formulas for games outside a team’s division were much more influenced by table position during the previous season.