Retrospective studies have shown improvement in migraines after patent foramen ovale (PFO) closure. To date, no study has evaluated whether the completeness of closure affects headache status; therefore, the objective of this study was to evaluate the impact of residual right-to-left shunt (RLS) on migraine symptoms after transcatheter PFO closure in migraineurs with and without aura. This was a small-series, single-center, retrospective analysis of late follow-up data on 77 patients with presumed paradoxical embolism and migraine who underwent PFO closure for secondary stroke prevention. Power M-mode transcranial Doppler was used to assess RLS at baseline and 6 and 12 months after closure. A standardized migraine questionnaire was administered at baseline and 6, 12, and 24 months after closure. Fifty-five (71%) patients had migraine with aura. Final closure and migraine status were available for 67 patients; 23 (34%) had incomplete PFO closure, defined as 30 embolic tracks detected at final power M-mode transcranial Doppler examination (median 366 days, 95% confidence interval 332 to 474). Migraine relief (≥50% reduction in frequency) was independent of closure status (77% complete closure vs 83% incomplete closure, p = 0.76) at late follow-up (540 days, 95% confidence interval 537 to 711). Migraineurs with aura were 4.5 times more likely to experience migraine relief than migraineurs without aura. In conclusion, migraine relief may occur despite residual RLS after transcatheter PFO closure, which may suggest a reduction in RLS burden below a neuronal threshold that triggers migraine; however, this warrants further investigation. Migraine with aura may be an independent predictor of relief after PFO closure.