The duo helped the Lionesses to a bronze medal in Canada in the summer while Heather Rabbatts is also honoured
Houghton captained the Lionesses at the World Cup in Canada where an impressive performance saw England come third, beating Germany 1-0 in the third place play-off.
Rabbatts, meanwhile, became the Football Association’s first female board member and has been honoured for her services to football.
There is also an award for Jaqui Oatley, the first female commentator on BBC’s Match of the Day, who receives an MBE for services to broadcasting and diversity in sport.
"I would like to congratulate Steph and Fara for their deserved honours,” chief executive Martin Glenn told the FA’s official website.
“Although football is of course a team game, they have both stood out for their remarkable individual contributions culminating in last summer’s World Cup in Canada.
"It was a privilege for me to be able to travel out to the finals and see at first hand just how committed they, and the rest of the squad, were to doing well for England.
“As captain, Steph has represented our Lionesses with distinction, leading from the front and setting the right example for others to follow.
"Fara has also had a year to remember, and away from the pitch has done much to inspire so many in her position as patron of the Homeless FA.
"Having both played pivotal roles in the superb third-place play-off victory against Germany, I am sure Steph and Fara will always look back on 2015 with great pride.
"On behalf of The FA, I would also like to pay tribute to Jacqui Oatley for the recognition she has received for her services to broadcasting and diversity in sport. She helped tell the Lionesses story to millions of viewers and has been a superb ambassador for the women's game over many years.
“Last, but not least, Heather Rabbatts has long been a powerful and informed voice in the game, especially in terms of championing the importance of football for all. Her honour is fully deserved and wonderful recognition for that unstinting service."