The defender was given the England armband and led Team GB at the Olympics in a year that also saw her perform impressively for Lincoln Ladies.
Stoney said: "I had a couple of names in my head that I thought would win it but my name wasn't one of those.
"I am in even more of a shock than when I first won it in 2008, especially off the back of such an important year. It was emotional and I was massively proud."
Stoney was also given a golden cap for appearing 100 times for the national team.