The English governing body has revealed in a statement that a safeguarding investigation in 2014 showed evidence of "inappropriate and unacceptable behaviour" from the 34-year-old.
It was initially ruled that Sampson "did not pose a risk" working in football, but it was only this week when the investigation was brought to the attention of the FA, which feels that the actions warrant a contract termination.
It has been stressed that the dismissal is in no way related to the allegations made by former England Women striker Eni Aluko, who claimed that in 2015 Sampson asked mixed-race midfielder Drew Spence how many times she had been arrested.
Aluko also alleged that in the year before, the national team coach advised the striker not to bring her family over from Nigeria due to concerns that they could be carrying the Ebola virus.
Sampson, who vehemently denies the allegations, was cleared of any wrongdoing by the FA, which "stands by" the findings of the two separate investigations.
The Wales-born coach, who was appointed England Women boss in 2013, guided the nation to two consecutive semi-finals at major competitions.