The Pipeline Embolization Device (PED) is an effective treatment approach for complex intracranial aneurysms. Intraprocedural complications during PED deployment are seldom reported. We report a rare complication of a PED malfunction identified immediately following complete deployment during endovascular treatment of a giant middle cerebral artery (MCA) bifurcation aneurysm. After multiple failed attempts at endovascular retrieval of the malfunctioned PED, the patient was taken for microsurgical extraction due to accumulation of thrombus on the proximal unopened portion of the stent and widespread distal dissemination of emboli. After removing the PED from the vessel lumen and resecting the giant aneurysm, we could not reanastamose the proximal MCA to the distal segment. The management of PED malfunction is poorly understood. While removal of an incompletely deployed PED may be undertaken with limited adverse effects, retrieval of a fully deployed PED is associated with a much higher risk of morbidity. Until larger case series of such complications better define the risks and benefits of endovascular or microsurgical retrieval of malfunctioned PEDs, the management of these rare intraprocedural complications will be based on the unique aspects of each individual case and the expertise of the treating neurointerventionalist.