The France international topped the poll of the 340-strong membership ahead of Blues team-mate Eden Hazard, with Tottenham midfielder Dele Alli in third place.
Between them, Blues duo Kante and Hazard, who was the 2015 Footballer of the Year, collected more than 65 per cent of the journalists' votes, which were spread over a record number of 17 different players.
Kante was instrumental in Leicester's shock Premier League triumph last season and following his £32million summer switch to west London, the midfielder looks set to collect a second successive championship medal with Chelsea now needing just two more victories to secure the title.
The 26-year-old will receive the prestigious FWA accolade, which has been awarded since 1948, at a gala dinner in London on May 18 when the association marks its 70th anniversary.
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.
The FWA said a record 17 players received nominations, with Kante and Hazard together sweeping up 65% of the votes cast. Five Chelsea players were nominated by FWA members, with David Luiz, Diego Costa and Cesar Azpilicueta also receiving votes.
A combo picture shows Chelsea's French midfielder N'Golo Kante (L) and Chelsea's Belgian midfielder Eden Hazard
Image credit: Reuters
FWA chairman Patrick Barclay said:
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.
The full list of players voted for is as follows: Sergio Aguero, Toby Alderweireld, Dele Alli, Cesar Azpilicueta, Diego Costa, Philippe Coutinho, Jermain Defoe, Ben Foster, Eden Hazard, Zlatan Ibrahimovic, Harry Kane, N'Golo Kante, Anthony Knockaert, David Luiz, Romelu Lukaku, Alexis Sanchez, Gylfi Sigurdsson.