Causes of thinning eyebrows. Even though heavy-handedness with a set of tweezers is a major cause of thin eyebrows, sparse hair on your brow line may not be your fault. Several conditions can contribute to the appearance of thinning eyebrows: 1  Nutrient deficiency. Vitamins A, E and D promote hair growth, and vitamin B mitigates bodily stress responses, which can prevent hair loss. 2  A deficiency in any of these vitamins can cause thinning eyebrows. 3  Hypothyroidism. 4  Interestingly, an under-active thyroid can cause women to lose one-third of the hair on their eyebrows.