The 23-year-old finally returned for Liverpool after 20 months out.
The Anfield side beat Exeter 3-0, despite not being able to overcome them in the original third-round tie. And the return of Flanagan - after some 20 months out injured - brought a smile to everyone's face in the red half of Merseyside.
Thompson personally congratulated the defender, whose passion and energy could make him the perfect player for Liverpool boss Jurgen Klopp.
Great to see young John Flanno back tonight,it's been a long tough road,well done mate— Phil Thompson (@Phil_Thompson4) January 20, 2016
Meanwhile, former Reds defender Rob Jones was impressed with the club's youngsters as a whole, who made an impression against Exeter at Anfield.
Indeed, Jones singled out four young Liverpool players - while also mentioning the return of Flanagan as a 'bonus' for Klopp's men.
The young lads showed some real individual class tonight from Brad & Kev to Cam & Ojo - And what a bonus it was to see @jon_flan93 back— Rob Jones (@RobjonesLFC2) January 20, 2016
The cup double is still on for Liverpool! Beating a lower-league side might not be the biggest of boosts after bitter defeat to Manchester United but the club's mediocre league form is counteracted by the fact they remain in both knockout competitions.
West Ham await the Reds in the FA Cup - sure to be a tough tie after the Hammers did the double over Liverpool in the Premier League - while Klopp's side hold a 1-0 aggregate advantage over Stoke City in the Capital One Cup semi-finals.