The Tottenham forward struck either side of half-time after Michael Keane had opened the scoring to ensure Gareth Southgate remains unbeaten as England Under-21 boss
Michael Keane opened the scoring from a Tom Carroll corner after five minutes and Kane struck either side of half-time as the Young Lions moved up to second in their European Under-21 qualifying group.
The visitors were convincing but rarely broke sweat against a San Marino side who never threatened a repeat of their historic heroics against Wales in September.
Southgate gave West Ham’s Ravel Morrison his first Under-21s start in a side which also boasted Raheem Sterling, Tom Ince and Carl Jenkinson.
San Marino, meanwhile, were without Juri Biordi, the man who scored the decisive goal in that famous victory over Wales, as they looked to claim a second successive scalp.
England started with intent and took just five minutes to dispel any fears of a shock – the scramble resulting from Carroll’s corner saw the ball fall to Keane, who fired in low.
The most trouble San Marino caused was a Lorenzo Liverani free kick which Jack Butland easily claimed, but more often it was England who threatened from their opponents’ set-pieces.
One such lightning counterattack set Sterling racing through on the right, but he blasted his shot high and wide in acres of space.
The pace, skill and combination play of Sterling and Ince tormented the home side, and on 29 minutes the Liverpool man headed poorly over from the Blackpool star’s hanging cross.
Five minutes later Sterling turned provider, racing down the right and curling in a pinpoint cross which Ince met on the half-volley, only to see his effort loop over the bar.
San Marino’s massed defensive ranks largely restricted England to long-range attempts, but on the stroke of half time Ince and Sterling combined to break them down again.
Racing onto the Blackpool star’s clipped diagonal ball in behind, the Liverpool youngster was brought down in the box by goalkeeper Andrea Manzaroli, who was promptly sent off.
Kane stepped up and found the net, though replacement stopper Massimo Francioni got a hand to his effort, and England led by two at the break.
Southgate’s men began the second half with unwavering purpose, and John Stones almost got lucky on 49 minutes when his mishit cross from the right struck the outside of the post.
With a man down, the San Marino defence seemed more hapless than ever, and two minutes later Morrison was afforded the freedom of the penalty area to force a low save from Francioni.
The stand-in goalkeeper seemed on a personal mission to keep the score down – first stooping low to deny Carroll, then deflecting Kane’s thumping header away from point-blank range.
There was nothing he could do on 65 minutes though, as Kane followed up on his own tame shot to give England a third after being played in by a rampant Sterling.
After scoring their third, England’s intensity dropped but Kane remained intent on getting his hat-trick, and with 15 minutes left the Tottenham youngster fired just wide from the edge of the box.
And in the dying minutes he got his wish, rounding Francioni from Carroll's lobbed pass and netting smartly from a narrow angle to compound San Marino's misery.