The striker celebrated his first start for the Under-21s with a hat-trick in the European U21 Championship 2015 qualifier in Serravalle.
Tom Carroll also started and played his part in two of the goals, delivering a corner for the opener and then a deft lobbed pass to set-up Harry's hat-trick goal two minutes from time.
Manchester United's Michael Keane opened the scoring after five minutes and Harry converted from the penalty spot after Liverpool's Raheem Sterling was brought down in first half injury time.
That resulted in a red card for San Marino goalkeeper Andrea Manzaroli.
England had to be patient against a team determined to sit in and defend and Harry broke through again on 64 minutes when he was sent clear by Sterling, saw his initial shot saved by substitute goalkeeper Massimo Francioni, before reacting first to fire home from a tight angle.
Harry's hat-trick goal was the pick of the bunch on 88 minutes. Again faced by a wall of San Marino defenders, Tom showed his vision by lifting the ball over the top for Harry to control and slide home from the right angle.
The pair now return home with the squad to prepare for Tuesday night's qualifier against Lithuania at Ipswich's Portman Road.
Meanwhile, Jordan Archer made a number of saves as Scotland Under-21s toppled Slovakia 2-1 at St Mirren.
Aaron McEneff played 90 minutes as Northern Ireland were beaten 2-0 by Belgium in the first of three qualifying matches for the European U19 Championships in Beringen, Belgium. Northern Ireland also play France and Iceland.