Background: Basilar invagination (BI) is a craniovertebral junction (CVJ) anomaly characterized by upward migration of the odontoid process into the foramen magnum. Congenital C1 occipital assimilation alters normal biomechanics and predisposes patients to instability. Trauma in such anatomically vulnerable individuals may precipitate acute neurological compromise, especially in pediatric populations. Aim: To evaluate the clinical presentation, radiological characteristics, and outcomes of trauma-induced basilar invagination in children with congenital C1 occipital assimilation. Methods: This retrospective study included 50 pediatric patients diagnosed with trauma-induced basilar invagination associated with congenital C1 occipital assimilation over a defined study period. Clinical data, imaging findings (CT and MRI), and management outcomes were analyzed. Radiological assessment included measurements using Chamberlain’s and McGregor’s lines. Results: The majority of patients presented with neck pain (78%), restricted neck movement (64%), and neurological deficits (42%). Imaging revealed odontoid migration above Chamberlain’s line in all cases. Surgical intervention was required in 60% of patients, while 40% were managed conservatively. Significant improvement in neurological status was observed in surgically treated patients (p<0.05). Conclusion: Trauma-induced basilar invagination in the presence of congenital C1 occipital assimilation is a rare but clinically significant condition. Early diagnosis with advanced imaging and timely intervention are crucial for favorable outcomes.