Pakistan Tehreek-e-Insaf (PTI) announced a series of protests from Friday
Manchester City's Kevin De Bruyne, Manchester United's Marcus Rashford and Liverpool pair Virgil van Dijk and Sadio Mane made up the rest of the top five.
The 30-year-old Henderson has been central to Liverpool's success under Juergen Klopp through his leadership and tireless midfield work.
"As grateful as I am I don't feel like I can accept this on my own. I don't feel like anything I've achieved this season or in fact during my whole career has been done on my own," said Henderson.
"I owe a lot to so many different people - but none more so than my current team mates - who have just been incredible and deserve this every bit as much as I do," he said.
Henderson has played in 30 of Liverpool's league matches so far this season and scored four goals.
Two other Liverpool players - right back Trent Alexander-Arnold and goalkeeper Alisson Becker - also received votes.
"I accept it on behalf of this whole squad, because without them I'm not in a position to be receiving this honour. These lads have made me a better player - a better leader and a better person," added Henderson.
"If anything I hope those who voted for me did so partly to recognise the entire team's contribution."
The Footballer of the Year trophy has been awarded since 1948 when Stanley Matthews was its first recipient.
Other players who received votes from FWA members included Raheem Sterling (Manchester City), Aaron Wan-Bissaka (Manchester United), Sergio Aguero (Manchester City), Adama Traore (Wolverhampton Wanderers), Danny Ings (Southampton), Jack Grealish (Aston Villa) and Leicester City pair James Maddison and Jonny Evans.
Pakistan Tehreek-e-Insaf (PTI) announced a series of protests from Friday
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