(1) Background. Bicuspid aortic valve (BAV) is associated with genetic defects (NOTCH 1, GATA 5) and aortopathy. Differences in the flow patterns and a genetic predisposition could also affect coronary arteries. The objective was to assess the coronary artery calcium score (CACS) and coronary artery disease (CAD) burden by coronary computed tomography angiography (CTA) in patients with BAV stenosis, as compared to stenotic tricuspid aortic valves (TAV). (2) Methods. A retrospective case–control study. A total of 47 patients with BAV stenosis (68.9 years ± 12.9, 38.3% females) who underwent CTA were matched with 47 TAV stenosis patients for age, gender, smoking, arterial hypertension, dyslipidemia, diabetes, body-mass-index and chronic kidney disease. (3) Results. The coronary artery calcium score (CACS) was lower in BAV (237.4 vs. 1013.3AU; p < 0.001) than in TAV, and stenosis severity was less (CAD-RADTM: p < 0.001). More patients with BAV had CACS zero (27.7% vs. 0%; p < 0.001). The majority (68.1%) of patients with BAV had no or non-obstructive CAD but only 25.5% of TAV (p < 0.001). Obstructive CAD (>50% stenosis) by CTA was more frequently observed in patients with TAV (68.1%; p < 0.001). (4) Conclusions and Relevance. Patients with BAV stenosis have markedly less coronary calcium and less severe coronary stenosis. CTA succeeds to rule out obstructive CAD in the majority of BAV, with adherent implications for TAVR planning.