The 26-year-old beat Blues team-mate - and 2015's winner - Eden Hazard to the prize, along with Tottenham striker Harry Kane, Alexis Sanchez of Arsenal, Manchester United's Zlatan Ibrahimovic and Premier League top scorer Romelu Lukaku of Everton.
Kante's latest honour comes with the France international on course to win back-to-back Premier League titles, having starred for Leicester City in last season's against-the-odds triumph. He will become the first player to achieve such a feat since the rebranding of England's top flight in 1992.
Chelsea's summer signing - a renowned as a tireless box-to-box competitor who helps break up opposition attacks and initiate them for his own side - was presented with the award at the Grosvenor Hotel in London on Sunday evening.
Tottenham midfielder Dele Alli was named Young Player of the Year for the second successive season, Manchester City's Lucy Bronze won the women's Player of the Year award for the second time having also won it in 2014, and Birmingham's Jess Carter topped the voting in the women's Young Player category.
Former England captain David Beckham received the PFA's Merit award for his contribution to the game.
Alli's young player prize is some consolation for his controversial omission from the six-man shortlist for the senior award.
The England midfielder, 21, has again been critical to Spurs' title push and heading into the weekend was the highest-scoring player in the league not recognised as a forward, with 16 goals.
England full-back Bronze won the women's player of the year award for the second time, after being part of the Manchester City squad which won the Women's Super League without losing a single game in 2016.
Birmingham midfielder Carter saw off competition from three Manchester City players to win the women's young player of the year award.
Beckham, who won 115 England caps and starred at club level for Manchester United, followed ex-Red Devils team-mate Ryan Giggs in winning the Merit prize. He also received the prize alongside his 'Class of 92' United team-mates in 2013.