Mitral valve prolapse (MVP) could associate with malignant ventricular arrhythmias (VAs). Mitral annular disjunction, a putative mechanism for an arrhythmic substrate, leads to excessive mobility, stretch, and damage of some segments. Speckle tracking echocardiography (STE), with particular attention to the segmental longitudinal strain and myocardial work index (MWI), could be an indicator of the segments we aimed to check. Seventy-two MVP patients and twenty controls underwent echocardiography. Complex VAs documented prospectively after the enrollment was qualified as the primary endpoint, which was noticed in 29 (40%) patients. Pre-specified cut-off values for peak segmental longitudinal strain (PSS) and segmental MWI for basal lateral (−25%, 2200 mmHg%), mid-lateral (−25%, 2500 mmHg%), mid-posterior (−25%, 2400 mmHg%), and mid-inferior (−23%, 2400 mmHg%) segments were accurate predictors of complex VAs. A combination of PSS and MWI increased the probability of the endpoint, reaching the highest predictive value for the basal lateral segment: odds ratio 32.15 (3.78–273.8), p < 0.001 for PSS ≥ −25% and MWI ≥ 2200 mmHg%. STE may be a valuable tool for assessing the arrhythmic risk in MVP patients. Excessively increased segmental longitudinal strain with an augmented regional myocardial work index identifies patients with the highest risk of complex VAs.