Background Vitamin D deficiency is a prevalent condition that is found in about 30–50% of the general population, and it is increasing as a new risk factor for coronary artery disease. Our study aimed to evaluate the relationship of serum vitamin D levels with coronary thrombus burden, Thrombolysis In Myocardial Infarction flow grade, and myocardial blush grade in patients managed by primary percutaneous coronary intervention for their first acute ST-segment elevation myocardial infarction. Results Eighty patients were included in the study with their first acute ST-segment elevation myocardial infarction and were managed by primary percutaneous coronary intervention. According to the serum concentrations of vitamin D, the study population was divided into 2 groups: group A with abnormal vitamin D levels less than 30 ng/ml (50 patients) and group B with normal vitamin D levels equal to or more than 30 ng/ml (30 patients). Angiographic data was recorded before and after coronary intervention. On comparing thrombus grade and initial and post-procedural Thrombolysis In Myocardial Infarction flow between both groups of patients, there was no significant difference (p = 0.327, p = 0.692, p = 0.397). However, myocardial blush grade was better in patients with normal vitamin D levels (p = 0.029) without a significant correlation between vitamin D concentration values and myocardial blush grade (r = 0.164, p = 0.146). Conclusions Patients with first acute ST-segment elevation myocardial infarction and normal vitamin D levels undergoing primary percutaneous coronary intervention had better myocardial blush grade and more successful microvascular reperfusion in comparison with patients with abnormal vitamin D levels. There was no significant difference between the normal and abnormal vitamin D groups regarding the coronary thrombus grade and Thrombolysis In Myocardial Infarction flow.