The women with atrial fibrillation (AF) were almost twice as likely to have fatal heart disease and strokes.
Women may respond less well to AF drugs or are being diagnosed later than men.
"One possibility is that women with AF are undertreated relative to men," Connor Emdin and colleagues, at the University of Oxford, told the BMJ.
In the meantime, experts say doctors should be aware of the findings in case more can be done to avert avoidable deaths.
About a million people in the UK have AF.
You can check if you might have it by feeling your pulse for about 30 seconds.
An occasional irregularity in pulse, such as a missed beat or extra beats, is common and nothing to worry about.
But if your pulse is continuously irregular with no pattern, you should see your doctor.
It may also be very fast, more than 100 beats per minute even when resting, leading to dizziness and shortness of breath.
Medicines can control AF and reduce the risk of a stroke (a clot or bleed in the brain).
In patients with AF, the heart's upper chambers - the atria - contract randomly and sometimes so fast the heart muscle cannot relax properly between contractions, reducing its efficiency.
June Davison, from the British Heart Foundation, said AF was under-diagnosed in both men and women.
"It is important that healthcare services for the prevention and treatment of AF take into account the different effects of gender on the condition," she said.
"More research is needed to find out more about the underlying causes of these differences."
Having an irregular heartbeat poses a greater health risk to women than men, a review of 30 studies, involving more than four million patients, suggests.