This report presents a rare case of ischemic stroke in a 16-year-old female, which was later diagnosed as being caused by protein S deficiency, a hereditary thrombophilia. Stroke at a young age is uncommon, and identifying the underlying cause is critical for proper management. The patient presented with right-sided weakness and slurred speech, with MRI confirming an ischemic infarct. Initial treatment with aspirin and atorvastatin was provided, but further investigations revealed low protein S levels, leading to the diagnosis. She was then managed with low-molecular-weight heparin (LMWH), followed by oral warfarin, resulting in significant neurological recovery. While inherited thrombophilias are uncommon causes of arterial strokes, this case underscores the importance of early identification and targeted treatment of such rare etiologies. Prompt initiation of anticoagulation therapy with LMWH followed by oral warfarin led to significant neurological improvement. This report highlights the need for thorough thrombophilia workup, individualized management, and the role of anticoagulation in improving outcomes, even in resource-limited settings.