Kante’s Chelsea team-mate Eden Hazard came second while Tottenham Hotspur’s Dele Alli finished in third position.
The 26-year-old France international only last month was named the winner of the Professional Footballers’ Association Player of the Year award.
Kante said: “It is a fantastic honour to win this award. With so many great players in this Chelsea squad and in the Premier League, for the Football Writers’ Association to name me their Footballer of the Year is a very proud moment in my career.”
FWA Chairman Patrick Barclay added: “N’Golo Kante could not be a more deserving winner of English football’s most prestigious individual award.
“In the view of some FWA members, he would have been a worthy recipient last season for his contribution to Leicester’s title success, but the almost unbroken excellent form of Chelsea since he changed clubs has left little room for further debate.
“Considering the competition of Eden Hazard and other players from Chelsea in particular, this is a great achievement.”