The Yorkshir man is charged with breaking Disciplinary Rule 66 and Disciplinary Rule 71 which guard against comments which bring the came into disrepute and those which are not in the "best interests" of the SFA.
Green was criticised by campaign group Show Racisim the Red Card this week after he was quoted in a newspaper report referring to former Ibrox director, Imran Ahmad, as his "little Paki friend".
Green has been given until Wednesday, April 17, to respond to the SFA's Notice of Complaint.
Speaking in an article in the Scottish Sun on Sunday, Green said: "I was brought up in a mining community where whether someone was black, white, Catholic, Salvation Army, Protestant, made no difference.
"When I played at Worksop Town, the other striker was 'Darkie' Johnson. Now if I say that today I could go to jail.
"You know, Imran will come into the office regularly and I'll say "How's my Paki friend?"
Following the publication of those comments, Green released a statement insisiting that he "deplores" racism and sectarianism, while accusing Show Racism the Red Card of a "knee-jerk reaction."
In a statement on Monday, he added: "It is unfortunate that Show Racism the Red Card has fallen into the trap of taking something out of context and giving a knee-jerk reaction.
"In the interview, I referred to the fact we are now living in a politically correct world where words and phrases that were once used are no longer acceptable.
"My use of the word 'Paki' was when I was referring to how I sometimes warmly address my colleague and friend Imran Ahmad when we meet, something we both know is light-hearted.
"I deplore racism and sectarianism and this football club does a huge amount of work in this area to help eradicate these problems."