The FPS, which began in England and Wales last July, enables people to block post, phone, email or text communications from named charities they no longer wish to hear from.
The Northern Ireland Council for Voluntary Action invited the regulator to operate in Northern Ireland last year.
Then, in October, the regulator and the Charity Commission for Northern Ireland signed a memorandum of understanding that enabled staff at the two organisations to cooperate on investigations and policy issues.
Registered charities in Northern Ireland that spend less than £100,000 a year on fundraising can sign up to the regulator for an annual fee of £50.
The 24 charities in Northern Ireland that spend more than £100,000 a year on fundraising have been asked to pay a voluntary levy of between £150 and £15,000 a year depending on how much the charity spends on fundraising.
As in England and Wales, the Fundraising Regulator will contact charities on behalf of members of the public and request selected methods of communication are stopped.
Charities must comply within 28 days or risk being referred to the Information Commissioner.
Walter Rader, board member for Northern Ireland at the Fundraising Regulator, said: "This is a vital step in continuing the work the Fundraising Regulator has undertaken to rebuild trust between the public and the sector over the last two years."
Frances McCandless, chief executive of the CCNI, said the FPS would help people "in making informed choices around the communications they receive from charities and helping to ensure charities are held to high standards".