Agenesis of the internal carotid artery (ICA) is a rare condition, whereas the association of this condition and the presence of intracranial aneurysms is higher in comparison to patients with normal vasculature. Endovascular treatment of this particular subgroup of patients has been described, but complications associated during treatment have not. Herein, we describe the endovascular treatment of intracranial aneurysms in two cases complicated with coil protrusion and in-stent thrombosis in the setting of agenesis of the ICA which were treated successfully without clinical compromise. One-year follow-up digital subtraction angiography demonstrated the complete obliteration of both aneurysms. In most of the cases, coil protrusion does not require further intervention; nevertheless, in the setting of ICA agenesis, stent placement is a potential alternative. In-stent thrombosis should be treated promptly with the available tools, in our case intra-arterial Alteplase reperfused the parent vessel.