Flanagan, who won the 2003 U.S. Amateur, finished the first round three shots ahead of Australians Brad Hughes, Andrew Tschudin, Ben Bunny and Michael Wright.
'I played exceptionally well today,' Flanagan said. 'I got away to a fast start which was good and then had a couple of lucky birdies on the back nine.'
The top four players in the two-round tournament ending Wednesday qualify for the Open, which will be played at Royal Liverpool in July.