Henderson began training in 1978 and is a four-time winner of the Champion Hurdle at Cheltenham where he has a particularly good record.
The Queen, a lifelong racing enthusiast, has 41 horses split between different trainers.
The jumps season is quiet at this time of year and Henderson has relatively few runners but as one of the sport's most established names, the embarrassment factor will likely be intensified through the royal connection.
The BHA said that in making its decision, its panel had taken into account various factors.
They included the fact the substance was administered by an experienced vet who Henderson considered as an advisor and also that the substance was unlikely to act as a performance enhancer.
It had also noted Henderson's contribution to the sport and his charitable activities.
The fine is double the previous record of 20,000 pounds handed to a trainer after Michael Wigham was penalised under the non-triers' rule last year.
HARSH SENTENCE
Henderson, who trains about 150 horses, said in a statement through the Press Association: "I am obviously hugely relieved that this saga has been concluded and, even though this seems a harsh sentence, we accept the findings and can now look forward again to the future and an exciting season ahead.
"Although the medication should not have been administered, I can only re-iterate, as the panel has accepted, that it was only given in the interest of the welfare of Moonlit Path herself."