Arsenal confirmed the injury occurred during their mid-season training camp in Dubai, with hopes he will return for pre-season in July.
It is a major setback for the Gunners, who are now without a recognised striker, with Gabriel Jesus also sidelined and both Bukayo Saka and Gabriel Martinelli injured.
The Gunners stated: “We can confirm that Kai Havertz has sustained a hamstring injury during a training session in Dubai last week.
“Subsequent assessments and specialist reviews have confirmed that the injury will require surgery, which will take place in the coming days. Soon after surgery, Kai will begin his recovery and rehabilitation programme, which is expected to extend into pre-season preparations for next season.
“Everyone at the club is fully focused on supporting Kai to ensure he is back to full fitness as soon as possible.”