Eilish McColgan, who is competing at the Games this summer, admitted she first suffered from palpitations at the age of 13.
But the 23-year-old is refusing to take beta-blockers or consider surgery - as it could hinder her chances of winning a medal.
McColgan was forced to cut short a trip to Qatar to see her mother, after her heart went out of beat for 36 hours.
UK athletics urged her to return home immediately for tests.
She now has to carry tablets with her at all times and has a specialist on speed dial should she begin to experience symptoms.
McColgan, who is competing in the steeplechase, said: “UK Athletics have been really good.
“They sent me to specialists, but the guy does not really know why it happened, what caused it, or whether it will happen again.
“The only way they can stop it ever happening again is to take medication every single day.
“But the problem is that beta blockers would slow your heart so much that you effectively just become slow in general life.
“I could go out for runs, but I wouldn’t be an athlete any more. I would have to just forget about that. So obviously he has said that isn’t an option.”
Her mother, Liz McColgan, is a former world 10,000m champion who won golds at the Edinburgh games in 1986 and Auckland in 1990.
She also won a silver medal at the 1988 Seoul Olympics.
Now known as Liz McColgan-Nuttall, she coaches in Qatar and also trains her daughter.
She said: “The problem may have been there all her days.
“But when she was here her heart went out of beat for 36 hours, and they couldn’t get it back.
“She wasn’t very well and it was a bit worrying.”
McColgan said her heart problem is similar to that which affected Olympic breaststroke silver medallist Michael Jamieson.
The Glasgow swimmers problems emerged after he pushed himself too hard in training, sending his heart into into an irregular rhythm.
Despite his condition, Jamieson, is one of the main medal contenders for Team Scotland at this years Commonwealth Games.
She added: I texted him and asked a few questions, he was really helpful and has had absolutely no issues since.
“I’m pretty confident, hopefully, that it was a one-off.
“It affected a good few weeks’ training and we’ve had to alter and adjust, make sure we’re doing the right things.
“Mainly it’s monitoring recovery sessions. We’re doing everything we can do to make sure I don’t have another episode.
“Fortunately, for the past four or five weeks I have been able to put in the training and don’t have any issues.”
Heart palpitations are heart beats that suddenly become more noticeable and can feel like your heart is pounding, fluttering or beating irregularly.
They can be triggered by a rush of adrenaline, spicy food, medicines or anxiety - in some cases they indicate arrhythmias, heart rhythm problems.
Common conditions include atrial fibrillation, which causes an abnormally fast heart rate.
A major cause of stroke, it affects 800,000 people in the UK, the majority of whom are aged 55 or over.