The 22-year-old will continue his rehabilitation programme under the guidance of the ECB medical team and is expected to focus on his recovery over the coming weeks.
Bethell was due to captain the Phoenix for the first time in 2026 and those duties will instead be handed to Donovan Ferreira, a senior player within the Phoenix ranks with experience tasting success in The Hundred.
Head Coach Shane Bond said: "We're all incredibly disappointed for Jacob and gutted he won’t be able to join us this year. It’s frustrating to lose a player of his quality, not least your captain, this close to the tournament but his long-term fitness has to be the priority.
“Everyone at the club wishes him the very best with his recovery and we look forward to seeing him back on the field as soon as possible.
“In Donovan Ferreira we have a real leader who knows what it takes to go deep into the competition. He’s won it before and will be a great person for the younger members of the squad to learn from. We’re lucky to have someone of his stature to step into the captaincy.”
Bethell added: "It's frustrating to miss out on The Hundred, especially representing Birmingham Phoenix in front of our supporters at Edgbaston. Unfortunately, I need to take the time to get back to full fitness.
"My focus now is on completing my rehabilitation and returning fully fit. I'd like to thank the fans, my teammates and the medical staff for all their support, and I'll be cheering the boys on throughout the competition."
Birmingham Phoenix will announce a replacement player for Bethell's position in due course.