Phytosterols in vegetable oils have gained attention for their nutritional benefits in foods and food supplements. However, the use of vegetable oils in emulsions for infant formulas and parenteral nutrition has raised some concerns, as phytosterols may contribute to phytosterolemia in the case of infant formulas and, in a second scenario, to parenteral nutrition-associated liver disease. The present study proposes removing phytosterols from soybean oil using a synthetic amorphous silica Trisyl® (E551) as an adsorbent material. The process is simple and involves stirring the oil at a high temperature under vacuum conditions followed by filtration to remove the adsorbent. A rotational factorial design of experiments, considering the adsorbent/oil ratio, temperature, and time was carried out to determine the optimal conditions. Additionally, the effects on tocopherols levels and formation of trans fatty acids were explored. The total sterol content in the initial refined soybean oil was 2540 mg/kg, with 32% in ester form (813 mg/kg). The treatments effectively reduced the sterol concentration, achieving a reduction of nearly 70% when 10% Trisyl®, 140 °C, and a 90-min treatment were applied. Under these conditions, nearly 80% of the oil was recovered. Campesterol and stigmasterol levels were almost halved. Tocopherol losses were found to be below 20%. Thermal degradation, as analyzed by triacylglycerol polymers and trans fatty acids, was not observed in the treatments.