The 28-year-old was diagnosed with the illness in December 2009 but had continued to play ever since, turning out for the Royals seven times this season.
However, after consulting with the club's medical staff, Armstrong has decided to call time on his playing days. "Obviously this has been a very difficult decision," Armstrong said.
"I absolutely love football but this is the right thing for me to do now. "It's right for me professionally, medically and also personally.
"With the illness, both the medical team and I didn't feel I could regularly perform to the level you have to in the professional game."