Transient hypothyroidism can present itself as clinically asymptomatic or with few symptoms. Early treatment with levothyroxine (L-T4) prevents complications related to this disorder. We report a case of a male infant with concomitant short bowel syndrome and transient hypothyroidism treated with rectal L-T4. A 4-month-and-10-day-old boy with previous gastroschisis underwent multiple surgical approaches for small bowel resection and developed short bowel syndrome. We suspected hypothyroidism because of jaundice (direct bilirubin up to 59 mg/dL), the absence of evacuation, oral diet intolerance, and intestinal dysmotility. Because of a thyrotropin level of 34.45 μIU/mL and a free thyroxine level of 0.64 ng/dL, the diagnosis was confirmed. Because fasting was demanding, we started the patient on rectal diluted L-T4. After 4 weeks, the patient had spontaneous peristalsis, improvement of jaundice (direct bilirubin: 4.6 mg/dL), and normalized free thyroxine and thyrotropin values. In the present case, the patient was diagnosed with hypothyroidism and was on absolute fasting. An alternative route of drug administration was warranted. We empirically prescribed rectal diluted L-T4 when intravenous and suppository L-T4 were not available. This method was proven to be safe and effective in improving the patient's clinical and biochemical status. Rectal L-T4 is a possible alternative route of administration to treat hypothyroidism in patients who are unable to take the medication orally.