The 24-year-old midfielder was due to start a week of rehabilitation at Lilleshall but had a relapse of his knee injury on Sunday.
Club physio Simon Shakeshaft confirmed that after a further examination by a specialist, he will now undergo reconstruction surgery on his cruciate ligament.
The Town physio confirmed on the SHREWSWEB "It's obviously a massive blow to Jags, but the long-term implication of an unstable knee will have more of determent to Jags career, and also damage to other structures in the knee is a distinct possibility."
Jagielka has been at Gay Meadow since August 1997 and made 35 first-team appearances in the season just finished before sustaining the injury against Swansea on March 5.