Fragmentation by pigtail rotation catheter may be a therapeutic option in acute massive pulmonary embolism, especially in patients with high risk of right ventricular failure. We report a patient with an occlusion of the right intermediate pulmonary artery by a large embolus, slightly protruding into the perfused right upper lobe artery. After initial catheter fragmentation, part of the embolus dislocated and produced an additional occlusion of the upper lobe artery. Hemodynamic parameters deteriorated. Continuation of catheter fragmentation finally provided for a hemodynamic stabilization and partial recanalization. Inadvertent occlusion of a major pulmonary arterial branch by dislocated embolus material may be considered as a complication of catheter fragmentation, which can be successfully managed by continuation of the fragmentation therapy.