The 30-year-old is entering the final year of his second contract with the club but wants a increase in salary after his level of production on the field increased, along with seeing fellow tight ends in the league receive big-money deals.
Davis wrote in his column for TheMMQB.com: "In 2010 I signed a five-year, $37m (£21.7m) contract extension with $23m (£13.5m) guaranteed. It was the biggest contract for a tight end in league history.
"Four years later, and I'm playing at a higher level than I was then, which brings me to why I'm holding out. It's all about getting paid what you deserve.
"It's not that complicated. I want the 49ers to win the Super Bowl, and I want to be on the field this summer working toward that goal, but I have to worry about my future first."
Davis recorded 52 receptions for 850 yards along with 13 touchdowns last season.