[3] Although the race was a five and a half furlong sprint, Persimmon was already being described as a potential Derby contender: as a brother to the stayer Florizel he was not expected to have stamina problems.

[6] Persimmon's final start of the season was in the Middle Park Stakes at Newmarket, one of the year's most prestigious two-year-old races, in which he was matched against another outstanding colt in St. Frusquin.

[8] On 11 October he started 2/1 favourite for the race, but never looked likely to win and finished third behind St Frusquin and the filly Omladina, beaten a total of four and a half lengths.

[9] Despite his defeat, Persimmon remained a leading fancy for the following year's Classics, and there was considerable speculation regarding the possible outcome of a rematch with St Frusquin in either the 2000 Guineas or the Derby.

His preparations for the Derby did not go smoothly: his performances in a demanding schedule[13] of exercise gallops were inconsistent,[14] and he was almost withdrawn after one particularly poor effort three weeks before the race.

[8] For the Derby at Epsom on 3 June, Marsh decided, perhaps in view of Persimmon's known temperament problems, to saddle the colt near the start, missing the traditional parade in front of the stands.

Ridden by John Watts, Persimmon was held up at the back of the field in the early stages as Bay Ronald and Gulistan made the running.

Watts moved him forward steadily and he turned for home in third place behind Bay Ronald and St Frusquin, and the race soon developed into a match between the first and second favourites.

St Frusquin had a slight advantage until the final furlong but Watts then made his challenge and Persimmon took the lead and ran on strongly to take the race by a neck,[15] winning rather more easily than the margin suggested.

[16] The first royal victory for more than a century was greeted with prolonged and "deafening"[17] cheering and "tremendous enthusiasm",[18] with the police having difficulty clearing a way through the crowds for the Prince to lead in his winner.

Starting at odds of 8/11, he pulled his way to the front half a mile from the finish and won the £10,000 prize very easily by two lengths from Sir Visto[23] This was a particularly impressive performance, with Persimmon showing "fire and dash" to win in the style of a top class horse.

Persimmon returned from the race very sore, reportedly because of the hardness of the ground, and was forced to miss an intended run in the Goodwood Cup.

In September, the managers of Lingfield Park Racecourse put forward a proposal for a £3,700 weight-for-age invitation race between the two Derby winners to take place over one mile on 2 October.