Graham was forced off after just 16 minutes of the game at Goodison Park after coming off worst in a challenge with Gareth Barry.
Scans revealed no serious problem but he is likely to miss City's back-to back games with Tottenham in the Premier League and Capital One Cup.
The 28-year-old would have sat out the league game against his parent club Sunderland at the KC Stadium on 2 November anyway but could be fit to return for the trip to Southampton a week later.
"Danny Graham is set to be sidelined for around three weeks with the injury he suffered in Saturday's game at Everton," read a statement on Hull City's official website.
"Although scans have revealed the striker escaped serious injury following a first half challenge by Gareth Barry, severe bone bruising around the knee will keep the on-loan Sunderland man out of action until next month.
"A return to action in our away game against Southampton is a possibility."