From Wiki:
Hypothalamic
Women who go through significant weight loss, dieting, or perform considerable amounts of exercise on a regular basis are at risk of developing hypothalamic (or 'athletic') amenorrhoea. It was thought for many years that low body fat levels and exercise related chemicals (such as beta endorphins and catecholamines) disrupt the interplay of the sex hormones oestrogen and progesterone. However, recent studies have shown that there are no differences in the body composition, or hormonal levels in amenorrhoeic athletes as compared to regularly cycling athletes. Instead, amenorrhoea has been shown to be directly attributable to a low energy availability. Many women who diet or who exercise at a high level do not take in enough calories to expend on their exercise as well as to maintain their normal menstrual cycles.
So, my guess is you are not taking in enough complex carbs. Even if you're not losing weight with much exercise, so staying on your TDEE with other sources of energy like fat or protein, can still cause this. Alongside to the complex carbs, take some non complex ones like fruit or sugar.
Do you eat a healthy carb meal before working out?
When I started working out I was low carb dieting and after some time I got all kind of symptoms. Sorry, I'm a man

, but just to point out the importance of good energy reserves. Symptoms where cramps, fatigue, bad cardio performance etc.
Eat more. Running takes enormous amounts of fuel from your system.
Hope this helps.