His father was Johnny Henderson who was one of the founders of the Racecourse Holdings Trust as well as earlier in life being Aide-de-camp to Field Marshal Montgomery. In 2005 two years after Johnny Henderson's death Cheltenham renamed one of the races at the Cheltenham Festival in his honour as the Johnny Henderson Grand Annual Chase. In 2006 Nicky Henderson won this race with a horse called Greenhope.
Henderson, educated at Eton College, has been a trainer since 1978, based at Seven Barrows near Lambourn, Berkshire. Previously he was an amateur jockey, and assistant trainer to Fred Winter between 1974 and 1978.
His most notable successes have come with See You Then, winner of the Champion Hurdle in 1985, 1986 and 1987; Remittance Man, winner of the Queen Mother Champion Chase in 1992; Punjabi, winner of the Smurfit Kappa Champion Hurdle in 2009 at the Cheltenham Festival, Binocular, winner of the 2010 Champion Hurdle, Long Run, winner of the 2011 Cheltenham Gold Cup and Bobs Worth, winner of the 2013 Cheltenham Gold Cup. Binocular's Champion Hurdle gave Henderson a fifth win in the race, equalling the record held by Peter Easterby. Zaynar, another horse he trained, also won at the 2009 Cheltenham Festival in the Triumph Hurdle. He was Champion Trainer in the 1985/86 and 1986/87 seasons. His record at the Cheltenham Festival is particularly good and amongst currently active trainer only Willie Mullins has won more races at the Festival than Henderson. His main stable jockey was Mick Fitzgerald until Fitzgerald was forced to retire by an injury sustained in the 2008 Grand National; from the 2008–09 season until the 2014–15 season Barry Geraghty was Henderson's principal jockey in Britain. At the start of the 2015–16 season Nico de Boinville became Henderson's principal jockey after Geraghty replaced Tony McCoy as the principal jockey of J P McManus.
One of Henderson's most popular horses in recent years, Caracciola, won the Cesarewitch Handicap flat race at Newmarket in 2008 at odds of 50/1 as an 11-year-old, despite mainly being a National Hunt horse. Caracciola followed up this success by winning the Queen Alexandra Stakes at Royal Ascot in 2009 as a 12-year-old with Eddie Ahern riding on both occasions. Henderson claimed his second winner at the famous Royal Ascot meeting when Veiled won the 2011 Ascot Stakes at 11/2. In 2013 Henderson had another important win with his horse Bob's Worth (Bought for only £20,000) continuing his unbeaten streak at Cheltenham with a win in the Gold Cup. This was despite Henderson raising concerns about the suitablily of the soft ground before the race started.
In June 2009, Henderson was found guilty by a British Horseracing Authority panel of breaching the rules of racing, after Moonlit Path, a mare he trains for the Queen, failed a drugs test. Henderson admitted to three of the four charges he faced in relation to the case, in which a prohibited anti-bleeding drug was found in the horse's bloodstream. Henderson accepted that the drug should not have been administered, but argued that it had been done so for the horse's welfare, and that he had not been attempting to enhance performance.
A further hearing was held in July 2009 to determine the sanction to be applied, and Henderson was fined £40,000 (a record penalty for the sport in the UK) and banned from running horses for three months (11 July to 10 October 2009). However, as Henderson is primarily a jumps trainer and this ban was during the flat season it caused him little inconvenience. He was allowed to continue training during the "ban" (which could more accurately be described as a suspension rather than a ban) but was not allowed to enter horses for the period of his ban. The majority of his flat horses were sent to his friend and fellow Lambourn trainer Barry Hills, highest profile of these horses being Caracciola. He caused a little controversy when he attended Royal Ascot when the horse ran but was not breaking any rules as he had not been "warned off" and he was a guest of Barry Hills.