The visitors took the lead early on through Michael Keane, who poked a shot past the keeper from close range after a corner had led to a goalmouth scramble.
England were forced to wait until first-half stoppage time for their second goal, which came from the spot. San Marino goalkeeper Andrea Manzaroli was sent off for a foul on Raheem Sterling, and Kane stepped up to double his side's lead.
Kane's second came in the 65th minute when he needed two attempts to beat sub keeper Massimo Francioni having been released by Sterling's pass.
The Tottenham Hotspur man completed his hat-trick in the closing stages of the match when he rounded the keeper before sliding the ball in from a tight angle having been found by a clever Tom Carroll pass.
Here, Sports Mole takes an in-depth look at an action-packed night of football in Serravalle.
On target 1
On target 13
Was the result fair?
Absolutely. England were dominant from start to finish and should have actually won by quite a bit more than the four-goal margin. San Marino never threatened Jack Butland's goal and had to rely on a mixture of poor finishing and good goalkeeping to keep the score down. England were always going to win this match, and there is no doubt that their performance was deserving of all three points.
San Marino's performance
As minnows of the world football stage, San Marino are always going to be underdogs going into a match no matter the age group. However, following their win against Wales in their last outing, spirits will have been high. After today's performance, they will still be high. They would have never expected anything from this match, but to keep the score down to four having been overrun for 90 minutes - 45 of which they had to play with 10 men - will be a source of pride for them. For their standards, it was a decent display.
In terms of general play, England were very good this evening. The likes of Raheem Sterling, Thomas Ince and Ravel Morrison ran the show in the first half and San Marino couldn't cope. The biggest problem for Gareth Southgate's side was sticking the ball in the back of the net. Their performance was so dominant that they should have scored double what they managed, and with more clinical finishing they could have even reached double figures. Southgate will be pleased with the performance and the win, but he will also take into account the quality of the opposition and the fact that there is still plenty of room for improvement.
Sports Mole's man of the match
Harry Kane: This one was very close between Kane and Sterling, who had a wonderful game before going off in the 65th minute. San Marino couldn't handle Sterling's pace and he created two goals and played a part in another as well. Still, you can't look past a player who scores a hat-trick in a game - and Kane could have had even more. The goals were his first for England Under-21s and, while three points were expected from the start, this is not a night that he will forget in a hurry.
Take your pick. England missed a plethora of golden chances, with Sterling, Ince and Morrison - among others - all at fault. There was also the referee's decision to send off the keeper, which was a very harsh one as Manzaroli appeared to get a large chunk of the ball. The biggest gaffe of the lot, however, was the referee's decision to book Sterling for a dive when the Liverpool winger was quite clearly taken out by a robust challenge. It was a very strange call from Eiko Saar and one that is almost impossible to justify.
As you may have gathered from the above paragraph, Eiko Saar did not have a good game. He got the majority of decisions wrong in the first half, including the big one in sending Manzaroli off. His booking to Sterling was made even stranger when he penalised Ince for diving later in the half but didn't show him a card. Those are just three of a number of poor decisions from the Estonian, who had a night to forget.
San Marino: San Marino will be looking for back-to-back wins over Wales when they face them again on Tuesday.
England: England, meanwhile, take on Lithuania on Tuesday as they look to remain unbeaten under Gareth Southgate.