The move comes in the wake of changes to the governance of Welsh universities, introduced by the Charities Act 2006, which will eventually see all universities in the principality register with the commission. They had previously been exempt from registration.
The university, which had an income of £415m in 2009, will become the seventh-largest charity registered with the commission by annual income.
Harry Iles, head of the Charity Commission’s Wales office, said: "Following registration, the public will be able to access information about the universities’ governance and accounts on our website in the same way as for all other registered charities, and this is invaluable for promoting a better understanding of the work they do."
He said the registration of universities would more than double the income of the Welsh charities regulated by the commission, from £1bn to £2.2bn a year.
Universities in Scotland are already regulated by the Office of the Scottish Charity Regulator. Most universities in England will not have to register with the Charity Commission and will continue to be regulated by the Higher Education Funding Council for England.
However, the colleges of Oxford, Cambridge and Durham universities will have to register with the commission. All student unions with incomes of more than £100,000 will also have to register.