Introduction: The aim of this study was to assess clinical outcomes and quality of life after PFO closure in patients with previous stroke/TIA of undetermined cause and in patients with other complex PFO-associated clinical conditions. Methods: Between July 2009 and December 2019 at our University Cardiology Department, 118 consecutive patients underwent a thorough diagnostic work-up including standardized history taking, clinical evaluation, full neurological examination, screening for thrombophilia, brain magnetic resonance imaging (MRI), ultrasound–Doppler sonography of supra-aortic vessels and 24 h ECG Holter monitoring. Anatomo-morphological evaluation using 2D transthoracic/transesophageal echocardiography (TTE/TEE) color Doppler and functional assessment using contrast TTE (cTTE) in the apical four-chamber view and contrast transcranial Doppler (cTCD) using power M-mode modality were performed to verify the presence, location and amount of right-to-left shunting via PFO or other extracardiac source. Completed questionnaires based on the Quality-of-Life Short Form-36 (QoL SF-36) and Migraine Disability Assessment (MIDAS) were obtained from the patients before PFO closure and after 12 months. Contrast TTE/TEE and cTCD were performed at dismission, 1, 6 and 12 months and yearly thereafter. Brain MRI was performed at 1-year follow-up in 54 patients. Results: Transcatheter PFO closure was performed in 106 selected symptomatic patients (mean age 41.7 ± 10.7 years, range 16–63, 65% women) with the following conditions: ischemic stroke (n = 23), transient ischemic attack (n = 22), peripheral and coronary embolism (n = 2), MRI lesions without cerebrovascular clinical events (n = 53), platypnea–orthodeoxia (n = 1), decompression sickness (n = 1) and refractory migraine without ischemic cerebral lesions (n = 4). The implanted devices were Occlutech Figulla Flex I/II PFO (n = 99), Occlutech UNI (n = 3), Amplatzer PFO (n = 3) and CeraFlex PFO occluders (n = 1). Procedures were performed under local anesthesia and rotational intracardiac monitoring (Ultra ICE) alone. The devices were correctly implanted in all patients. The mean fluoroscopy time was 15 ± 5 min (range = 10–45 min) and the mean procedural time was 55 ± 20 min (range = 35–90 min). The total occlusion rate at follow-up (mean 50 months, range 3–100) was 98.1%. No recurrent neurological events were observed in the long-term follow-up. Conclusions: The data collected in this study demonstrate that percutaneous PFO closure is a safe and effective procedure, showing long-term prevention of recurrent cerebrovascular events, significant reduction in migraine symptoms and substantial improvement in quality of life.