The electric wing, who has a major part of the under-20s charge to their third-place finish at the recent Junior World Championships, will undergo surgery on the weekend.
He is expected to be sidelined for up to four months, with a comeback pencilled in for the end of October.
"Eli Walker will miss the start of the 2012/13 season after it was confirmed that he will undergo surgery this weekend to repair shoulder ligaments," said a statement released by the Ospreys.
"After an initial couple of days to recuperate from surgery, Eli will commence a programme of daily treatment and rehab next week, with the target of a return to action around the end of October."
The 20-year-old from Swansea established himself a regular at the Liberty Stadium last season and made 14 regional appearances.
He scored two tries during the campaign, including a dazzling solo effort against Ulster at Ravenhill in February.
Walker was rewarded for his regional form with a place in Danny Wilson's squad for the World Championships in South Africa.
He was one of the stand out players in the Rainbow Nation and bagged two tries in four games as Wales secured their highest ever finish.