The primary culprit for this abysmal winning percentage is due to the fact that from 1978 to 1996, including two Super Bowl losses, the Bengals dropped nine straight games in the series. Six of those nine losses were by single digits, with half of those by a field goal or less.
After two decades of losing every game in the series, the Bengals won a pair of high scoring shootout victories. In 1999 the Bengals won 44-30 behind a 334 yard, four touchdown performance by Jeff Blake. And in 2003, Rudi Johnson cranked out a pair of touchdowns and 174 yards on only 21 carries, as the Bengals won by a score of 41-38.
Unfortunately the series has taken a negative turn as the last two games between the Bengals and 49ers have been close losses.
2007: Bengals 13, 49ers 20
The 2007 game looked like one that sat in the Bengals' favor, as they were facing a bad 3-10 49ers team.
Looking back, the offense did everything you'd want from an efficient team. Carson Palmer had a good game with 252 yards, a touchdown, and zero sacks. The offense converted 50% of their third down conversions, had zero penalties, and zero turnovers. Despite that, they only scored 13 points.
Unfortunately the Bengals' defense could not keep the 49ers off the field to give their offense a chance to score. The Bengals allowed an average of 9 plays per 49ers possession, and forced only one three-and-out the entire game. The Bengals allowed the 49ers third string quarterback, Shaun Hill, to complete 75 percent of his passes. The Bengals' defense also allowed the 49ers to convert a ridiculous 71 percent of their third down conversions, while forcing zero turnovers.
2011: Bengals 8, 49ers 13
The 2011 Bengals vs 49ers matchup was the first one that could have given fans a taste of Dalton facing Kaepernick, the two quarterbacks who have been loosely tied together since being drafted back to back in the 2011 NFL draft. But Kaepernick spent the 2011 season sitting on the bench, attempting only four more passes and one less touchdown than David Akers, the 49ers' kicker that season.
The 2011 game featured a 49ers team who ultimately finished 13-3 and reached the NFC championship game, ultimately losing in overtime to the New York Giants. Meanwhile, the Bengals were breaking in a rookie quarterback, and were projected by many to finish among the bottom rungs of the NFL ladder.
After scoring a field goal on their opening drive, the first half quickly devolved into a rough defensive struggle, with both teams punting on the remaining nine drives of the half.
With 10 minutes remaining in the game, the Bengals held a slim 6-3 lead, with the two teams combining for 14 punts on their first 18 possessions.
The first touchdown was finally scored with 4 minutes remaining, when Kendall Hunter ended a 49ers' drive on a seven yard run.
On the Bengals' next possession, Dalton was picked off, which led to a 49ers' field goal, and a 13-6 lead. Four plays later, Dalton threw another interception. Dalton's second pick was inside of two minutes, and all but secured the 49ers' victory, as they ate up as much clock as possible before allowing a safety with 8 second remaining, which resulted in the 13-8 final score.
2015: Bengals vs 49ers
Four and a half years after being drafted back to back, the 2015 matchup between the Bengals and 49ers looked like it would finally give us the matchup between Dalton and Kaepernick. That won't be happening. Suffering through a second, consecutive sub-par season, Kaepernick was benched before being placed on season ending Injured Reserve with a shoulder injury. For the Bengals, Dalton injured his thumb last week and won't play in San Francisco, though he will make the trip to support backup turned starter AJ McCarron. The 49ers are among the worst teams in the NFL and just lost to the Browns. While an Andy Dalton-led Bengals team would have been heavy favorites in this game, the Bengals are still favored in San Francisco, but to a lesser extent.