On September 4, 2018, he joined the Reebok Boston Track Club in Charlottesville, Virginia to be coached by Chris John Fox.

[5] Flanagan made his professional debut on January 26, 2019, at the Dr. Sander Columbia Challenge at the Armory in New York City.

Competing over 10,000 m, he set a personal best of 28:19.51 in Palo Alto on May 2 and would go on to win the Canadian title in the event the next month in Burnaby.

He achieved the necessary world ranking but was beaten out for a spot on the Canadian team by Moh Ahmed, Justyn Knight, and Luc Bruchet.

[7] The next week, he announced that he had signed a contract with On and was moving back to Ann Arbor to train with the Very Nice Track Club under coach Ron Warhurst.

[11] Flanagan opened his season on January 27 with a personal best of 13:11.97 over 5000m at the BU John Thomas Terrier Classic.

At the B.A.A 5K in April, Flanagan broke Charles Philibert-Thiboutot's Canadian record in the 5 km road race running 13:26, finishing second behind training partner Morgan Beadlescomb.

[12] Later that summer, he qualified to represent Canada at his first World Athletics Championships in the 5000m where he finished 11th in his heat with a time of 13:38.69[1] In October, he represented Canada in the inaugural 5 km road race at the 2023 World Athletics Road Running Championships in Riga, Latvia finishing 12th in a time of 13:34.

On January 26, Flanagan entered the 5000 m at the John Thomas Terrier Classic in Boston with the goal of achieving the Olympic standard of 13:05.00.

After his brief indoor season, Flanagan embarked on a six-week altitude camp in Boulder, Colorado, training alongside members of the On Athletics Club in preparation for the Sound Running TEN on March 16, a 10,000 m race in San Juan Capistrano, California.