Surgical re-implantation of the left coronary artery (LCA) is the treatment of choice in anomalous origin of left coronary artery from pulmonary artery (ALCAPA). Despite normalization of left ventricular function after surgery, residual coronary lesions or myocardial fibrosis may be found. The aim of this study was to detect regional left ventricular dysfunction predictive of coronary lesions or residual myocardial fibrosis using speckle tracking. We enrolled ten patients treated with surgical re-implantation of LCA for ALCAPA. All patients were asymptomatic, and ejection fraction (EF) was normal. Using S-SR imaging, we studied longitudinal, radial, and circumferential function. A cardiac MRI was performed to assess myocardial fibrosis and the anatomy of the coronaries. In case of suspected coronary stenosis, a coronary angiography was performed. Finally, 20 normal subjects were enrolled as control group. Median age at surgery was 188 days, and mean follow-up was 8.7 ± 4.7 years. Longitudinal and circumferential functions were reduced in LCA territory compared to RCA territory and normal. MRI showed LCA stenosis in three of ten patients, confirmed by coronary angiography: these patients had the lowest longitudinal strain values in LCA territories (−11.7, −14.7 and −14.8%). Radial strain was preserved (Normal 45.6 ± 12.1, ALCAPA 43.5 ± 10.7%, p = ns), while circumferential strain was mildly depressed (−23.5 ± 3.8 vs. −20.3 ± 2.0%, p < 0.05). After LCA re-implantation, ALCAPA patients showed a residual sub-endocardial damage in LCA territories. Despite a normal systolic and diastolic function, the prevalence of residual coronary lesions was high. A mean longitudinal strain >−15% in LCA territories was able to identify those patients.