For the first time, the Queen has stepped inside a Roman Catholic church on the island of Ireland in what is being seen as a hugely symbolic moment, reports Sky News.
Her Majesty was cheered as she waved to the crowds outside St Michael's Church and then those inside clapped as she entered the building.
Earlier in the day, the Queen attended a thanksgiving service at an Anglican cathedral in the town, on the eve of her historic handshake with Deputy First Minister and alleged former IRA commander Martin McGuinness.
Eleven people died in the IRA bombing of the war memorial on Remembrance Sunday 1987.
After the thanksgiving service, the Queen was thought to have met the families of some of the victims.
Her arrival in the province was delayed by almost an hour after bad weather forced the royal flight to divert from Enniskillen to Aldergrove Airport, near Belfast. Hundreds of people lined the streets of Enniskillen to greet the Queen and the Duke of Edinburgh as they made their way to the cathedral in a chauffeur-driven car.
A trumpet fanfare marked their arrival in St Macartan's Cathedral through its west door, where they were welcomed by the Dean of Clogher, the Very Reverend Kenneth Hall.