Although officially representing Great Britain, Daly saw himself as an individual representing Ireland. In 1906 Daly and two other athletes, Con Leahy and Peter O"Connor, were entered for the Intercalated Games in Athens by the IAAA and Gaelic Athletic Association, representing Ireland. They were given green blazers and caps with a gold shamrock, and an Irish flag (the Erin Go Bragh flag).
However, the rules of the games were changed so that only athletes nominated by National Olympic Committees were eligible.
Ireland did not have an Olympic Committee, and the British Olympic Council claimed the three as their own. In what became the first political protest in modern Olympic history, O"Connor, who came second in the long jump, scaled the flagpole, and removed the Union flag, replacing it with a green flag.
Daly stood guard at the bottom of the pole, while Irish and American fans kept security guards at bay. At those Games Daly finished third in the 5 mile competition, but was disqualified for obstructing Edward Dahl.
He abandoned his marathon race after 18 miles due to blisters and an ankle injury, which resulted in a three-day hospitalisation.
After 1906 Daly mostly raced in the United States, where he later became a successful New York businessman. He was selected for the 1908 British Olympic team, but did not compete. In 1907 he enjoyed his greatest successes, winning the 5 mile and 10 mile United States. A.A.U. titles and the Canadian 3 mile title.
In 1909, running for the Irish American Athletic Club, he came in second place in the Yonkers Marathon, in a time of 2 hours 55 minutes and 44 and 4/5 seconds.