The decision comes as some clinicians warned it could put patients at risk.
The unit would carry out complex vascular surgery for potentially life-threatening conditions like abdominal aortic aneurysms.
However, Betsi Cadwaladr University Health Board said this only represented about 20% of its vascular treatments.
The health board insisted the majority of its vascular services would still be carried out at the other hospital sites across north Wales, including Ysbyty Gwynedd in Bangor and Wrexham Maelor Hospital.
"Currently, around 300 complex vascular surgery operations are carried out each year in North Wales - representing about 20% of our vascular activity - and we are committed to continuing the majority of our work at Ysbyty Gwynedd, Ysbyty Glan Clwyd and Wrexham Maelor Hospital," said Dr Evan Moore, the board's executive medical director.
"Units such as these - which provide a hub for major vascular arterial operations - are being created across the UK, and there is strong evidence that such sites improve clinical outcomes and patient safety, whilst attracting the best staff and help to develop the best infrastructure."
Vascular medicine covers a wide range of medical procedures and interventions, from screening for risks of aneurysms - where weakened walls of major blood vessels could burst - to treating varicose veins, stroke prevention and helping ensure dialysis patients can continue their treatment.
But speaking ahead of the announcement, one consultant physician at Ysbyty Gwynedd raised concerns.
"This is an integrated service, and other aspects of what we do here would be threatened - radiology, urology and gastroenterology to name just a few," Dr Mahdi Jibani told BBC Wales.
Ken Jones of the North Wales Kidney Association added: "If this service goes, it will cost lives, there's no two ways about it."
Arfon assembly member Sian Gwenllian said it represented "yet another example of services creeping eastwards".
But Dr Moore argued that far from hitting services at other hospitals in the region, vascular services would benefit from a specialised hub.
"Hubs such as the one we have planned, built on the considerable knowledge, skills and practices already here, would protect connected services at these locations.
"These include outpatient consultations, investigations, diagnostic procedures, varicose vein and day case surgeries. It will also ensure strong support for other services such as accident and emergency, urology surgery and renal therapy."

The images were taken by architect Dennis Calow during the city's regeneration from the mid-1950s to the 1970s.
The collection has been added to an online map created by the University of Leicester.
It is hoped it will inspire other people to share photos and memories.
Dr Simon Dixon, archives manager at the university, said at least 12,500 buildings and homes were demolished in Leicester when the clearance of working class Victorian housing resumed after being interrupted by World War Two.
He said Dennis Calow was interested in the historical value of pre-20th Century buildings due to be torn down.
Mr Dixon said the project was inspired by the growing number of Facebook pages dedicated to historical photos of cities.
He said he hoped the photos would encourage people to come forward to share information about Leicester's lesser-known lost buildings.

The 38-year-old sank 10 birdies but bogeys on the 10th and 15th prevented him building a bigger advantage.
Compatriot Jamie Lovemark is in second place after shooting a round of 65.
Five-time major winner Phil Mickleson, also American, climbed the leaderboard with a 66 and trails Dufner by six.
Scotland's Martin Laird made the cut after a 69 moved him to 10 under par but England's Luke Donald (71) missed out.
Health chiefs in north Wales have confirmed plans to site a specialist vascular unit at Glan Clwyd Hospital in Denbighshire.
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Hundreds of photos of buildings demolished during Leicester's post-war slum clearance programme have been published online.
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American Jason Dufner heads into the final round of the CareerBuilder Challenge with a two-shot lead after carding an eight-under-par 64 in California.