Septic thrombosis of the lateral sinus is a rare complication of otitis media; currently, it hasn't been found a case report of septic thrombosis of the lateral sinus in the medical literature of Colombia and, in addition to this, there is no consensus in the management of this pathology. Hence the importance of the present case, which is a 3-year-old male patient, who presented a clinical picture of 7 days of evolution characterized by right otalgia and fever, which after the administration of amoxicillin for 5 days got complicated and showed symptoms of severe headache, photophobia, nausea and vomiting. An extra-institutional computed tomography was performed, where thrombosis of the right lateral sinus and bilateral mastoiditis was evidenced, therefore it was remitted to the Misericordia Hospital in Bogotá, Colombia, where the treatment with intravenous ceftriaxone started, it was requested a magnetic resonance that confirmed the diagnosis and it was decided to perform right mastoidectomy and tympanostomy with ventilation tubes insertion, after this the patient was treated with low molecular weight heparin for 3 months and, in the long term, he presented a favorable evolution.