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.
Calling it quits: Armstrong (right) played for a number of clubs during his career, including Sheffield United
'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.'
Despite his career being cut short, Armstrong feels he has been fortunate to be involved in football and paid tribute to Reading for helping prolong his playing time.
'I've been very fortunate to play for Reading and all my other clubs,' he added.
'I've been lucky to have a career that I know many people would be delighted to experience. I'll miss being a part of the game on a daily basis.
'At Reading I've worked with some fantastic people and I would like to thank the manager and all the staff, especially the medical team for helping me so much to get back playing; at one point I didn't think that would be possible.'
Armstrong, who previously enjoyed spells with Blackpool and Sheffield United among other clubs, made 47 appearances during his three years with Reading.
Manager Brian McDermott paid tribute to the defender, adding: 'Chris has been an inspiration to me.
'Over a long period I've had many conversations with him, he's a quiet, unassuming man who absolutely sums up everything that is good about human beings.
'Nobody could have tried harder and given more than he has given. It is important that Chris knows that I personally, and I am sure I can speak for all the staff and players, will always be there for him any time he needs us.'
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