Myocardial perfusion-single-photon emission computed tomography (MP-SPECT) is used to evaluate microvascular dysfunction and coexisting coronary artery disease in patients with hypertrophic cardiomyopathy (HCM). Phase analysis in gated MP-SPECT can provide additional information on left ventricular (LV) dyssynchrony, while the extent of late gadolinium enhancement (LGE) on cardiac magnetic resonance (CMR) imaging is an important prognostic factor in patients with HCM. We, therefore, sought to investigate the relationship of dyssynchrony by phase analysis on gated MP-SPECT and LGE on CMR imaging in 22 patients with HCM who underwent both stress/rest-gated MP-SPECT and contrast-enhanced CMR imaging. LV dyssynchrony parameters [phase standard deviation (SD) and histogram bandwidth] from gated MP-SPECT were compared with LGE parameters from CMR imaging [L/C contrast and %LGE calculated, respectively, as LGE intensity/LV cavity intensity and (LGE volume/myocardial volume) × 100]. Phase SD and histogram bandwidth showed strong correlation with %LGE (r = 0.73, p < 0.0001 and r = 0.73, p < 0.0001, respectively), although they did not significantly correlate with L/C contrast (r = 0.30, p = 0.17 and r = 0.26, p < 0.25, respectively). The LV dyssynchrony derived from gated MP-SPECT strongly correlated with the extent of LGE on CMR imaging. In conclusion, our investigation suggests that gated MP-SPECT may be useful not only for the assessment of myocardial ischemia but also the extent of myocardial replacement fibrosis.