The islands, located off the coast of Cornwall, began the scheme two years ago to protect eggs and baby birds from being eaten by brown rats.
Numbers of manx shearwaters and storm petrels had declined by 25% on St Agnes and Gugh in 25 years.
But colonies are recovering thanks to the rat eradication measures.
Poison placed in an agricultural pipe was positioned in 1,000 locations on the islands in order to kill the vermin.
According to international protocols, the islands could not be officially declared rat-free for two years after the last sign of rat was detected - making them officially free of the rodent on 13 February.
Jaclyn Pearson, from the RSPB Isles of Scilly seabird recovery project, said the seabird population was already starting to recover.
"Straight away we saw results," she said.
"The baiting was done in winter 2013, and in September 2014 we had 10 Manx Shearwater chicks. That's the first time in living memory that chicks have survived and it's clearly because of the removal of the rats.
"We didn't think we would have an uptake of storm petrels so quickly as they hadn't nested on the island for a long time, but we recorded five in 2015.
"So already the results are clear and they're beginning to bounce back."
A questionnaire among residents shows they're delighted with the results, the RSPB said.
The project cost Â£700,000 and was funded by the Heritage Lottery Fund and the European Union.
Wildlife Management International Limited (WMIL) from New Zealand was contracted to carry out the rat removal phase from November to March in "the most humane way".

The World Athletics Gala was scheduled for Saturday, 28 November in Monaco.
However, Lord Coe, president of the International Association of Athletics Federations, said: "This is not the time for the athletics family to be gathering in celebration of our sport."
The male and female athletes of the year will now be announced online.
Coe added: "We will rightly still honour the outstanding achievements of the sport's athletes.
"Therefore the athlete of the year and other annual honours will still be awarded and will be promoted and announced on the internet and social media.
"The IAAF will seek a suitable occasion in the future for the presentation of these awards to be made to the winners."
British distance runner Mo Farah, who won the 5,000m and 10,000m double at the World Championships, is nominated for the athlete of the year award.
Among others, Farah is joined on the list by Jamaica's Usain Bolt, who claimed the 100m and 200m sprint double in Beijing and Dutch sprinter Dafne Schippers, who won 200m gold and 100m silver.
The gala is run by the IAAF's own charitable foundation and Coe had to ask the foundation to cancel it, as it is not under the IAAF's control.
Diack remains under investigation by French prosecutors, with the 82-year-old under suspicion of receiving money in 2011 in return for deferring sanctions against Russian athletes who failed drug tests.
Diack, who was IAAF president from 1999 to August of this year, is yet to comment on the allegations.
Meanwhile, four men, including the son of former president Lamine Diack, have been charged by the IAAF with breaching its code of ethics.
Two of the Isles of Scilly have been declared "rat free" after a scheme to protect sea birds saw more than 3,000 rodents culled.
[NEXT_CONCEPT]
Athletics' annual awards ceremony has been cancelled by the sport's governing body in the wake of investigations into former president Lamine Diack.