The 20-year-old has managed the injury for about 18 months, but has now been forced to arrange an operation.
"I'm not looking forward to this, but it has to be done if I want to continue my career in the best possible way," Clayton told BBC Radio Jersey.
"I probably missed five events with it, so it will help in the long run."
Clayton - who, along with James Connelly,  - first suffered the injury at the Under-18 British Championships in 2012, an event he went on to win.
He had painkilling injections in his shoulder, but the problem flared up again during pre-season and after his first tournament of the year, he has decided to follow medical advice and have the operation.
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"My specialist said the rehab programme was really good and I've been doing the right things.  I built up the muscles well and it's down to that that I kept playing for so long.
"But my serve was really affected by it in the tournament I just played and I was struggling to generate pace. The serve is one of, if not the, biggest part of the game so I really need to sort it out," he said.
"I'm still young and I don't have points to defend until the end of the year really, so it's the best time to do it, even though there's never a good time to have it happen.
"I'm in a better place than I was this time last year mentally, physically and in terms of my playing ability, so I'm going into it with the right frame of mind and I just need to get it sorted."                                        ."

It was found by a submersible vehicle at a depth of around 2.5 miles (4km) off Necker Island.
Scientists from the National Oceanic and Atmospheric Administration (NOAA) said it was a depth record for an octopod without fins.
The creature has already been nicknamed "Casper" after the cartoon ghost.
The octopod lacked pigment cells, giving it its light-coloured appearance.
"It is almost certainly an undescribed species" Michael Vecchione of the NOAA said, calling it a "remarkable little octopod".
Deep-sea octopods fall into two categories - cirrate, or 'Dumbo', octopods with fins, or incirrate octopods, without fins, which look more akin to shallow-water octopus.
The sighting of Casper represents the deepest ever observed sighting of an incirrate octopod, Mr Vecchione said.

Emily Arbuthnott, 37, struck James Lyall, 82, while he was walking across the road in front of her car at a zebra crossing on the A92 in Inverbervie in November 2014.
Mother-of-three Arbuthnott, of Laurencekirk, admitted the charge at Aberdeen Sheriff Court.
Sentence was deferred for background reports.
The charge stated the driver failed to slow down or stop when her vision was obscured by the sun and did not notice Mr Lyall as he crossed the road.
He was taken to hospital in an ambulance under police escort but later died.
Arbuthnott, the daughter-in-law of the 17th Viscount of Arbuthnott, was not injured in the crash which happened on 5 November 2014.

It follows an incident in which a member of staff was threatened with what was believed to be a firearm at the shop in Frizington in October.
Paul Roger Farish, 18, of Moor Place, Frizington, appeared before West Cumbria magistrates charged with robbery and possessing an imitation firearm.
He was remanded to appear before Carlisle Crown Court on 7 December.
A second man, aged 19, who was also arrested, has been released on police bail until 14 December.
Jersey tennis player Scott Clayton faces up to six months out of the sport as he prepares to undergo surgery on a longstanding shoulder injury.
[NEXT_CONCEPT]
Scientists say a translucent, "ghost-like" octopod discovered in ocean depths near Hawaii is "almost certainly" a new species.
[NEXT_CONCEPT]
A motorist has admitted causing the death of a pensioner by driving carelessly on an Aberdeenshire road.
[NEXT_CONCEPT]
A man has been charged with robbing a post office in Cumbria.