Prime Minister and Minister for Marine Resources Henry Puna signed the agreement after meeting with the Solicitor General David James and Secretary of Marine Resources Ben Ponia.
The signatory on behalf of the EU is the current President of the Council of the European Union, Donald Tusk.
Under the Partnership, the Cook Islands will receive nearly $US7 million over a 4-year period in return for providing access to four European flagged purse seine fishing vessels which will target the migratory and abundant skipjack tuna.
The agreement includes a protocol to fish up to 7,000 tonnes per annum - around 156 fishing days or 12 per cent of the Cook Islands' 1250 fishing day quota set by the Western and Central Pacific Fisheries Commission.
The financial returns of the SFPA exceed other bilateral arrangements, including the US Fisheries Treaty package.
The agreement provides for the ministry to partner with the Spanish purse seine industry and World Wide Fund for Nature on a fisheries improvement plan that aims to have tuna catches sustainably certified under the Marine Stewardship Council accreditation processes.
In addition, the government will receive $1.8 million to support the fisheries sector which it intends to invest in initiatives such as a modern fisheries surveillance facility and subsidies for local fishermen.
The Ministry said it remained committed to best practice precautionary management of stocks in their exclusive economic zone to ensure stocks remain healthy and to maximise the ecological and economic benefit in the long term.
Mr Ponia said his ministry is now preparing to move forward with implementation of the Partnership.
The Cook Islands opposition has previously said the process of ratification had not been properly conducted while the foreign ministry warned the agreement contained "fatal flaws", compromising the Cook Islands' right to manage its own affairs without outside influence.
Community groups had also marched in protest against the agreement.