Objective To summarize the clinical features and MRI manifestations of the acute onset of mitochondrial encephalomyopathy (ME) in children, so as to improve the understanding of the disease. Methods The clinical and imaging data of 12 children with confirmed ME from March 2018 to December 2021 were retrospectively analyzed. Results Twelve cases of ME were included, 5 males and 7 females, with a median age of 8 years and 6 months. The main symptoms included stroke-like episodes (8 cases, 66.7%) and headache (7 cases, 58.3%); laboratory tests showed increased serum lactate in 10 cases (83.3%), and genetic testing was positive in 9 cases (75%). 11 cases of cranial MRI scanning detected the lesion, and the lesion areas all showed large patchy T1WI low signal, T2WI/T2-FLAIR high signal, of which nine cases involved cortical and subcortical regions, with the temporoparieto-occipital lobe being the most susceptible area, and the other two cases symmetrically involved the basal ganglia/brainstem and cerebellar hemispheres/brainstem, and six cases were combined with cerebral atrophy; diffusion-weighted imaging (DWI) in seven cases showed that the diffusion of the disease was limited in six cases; magnetic resonance angiography (MRA) in four cases showed that there was an increase in the number of branches of the middle cerebral artery of the affected side; arterial spin labelling (ASL) in three cases showed that the lesion area was highly perfused; and MRS in six cases suggested that the lesion area was highly perfused; and spectroscopy (MRS) suggested that elevated lactate peaks were detected in the lesion area in six cases. Conclusions The most common clinical symptoms of ME in children are stroke-like episodes. Genetic testing may be negative in a few cases, and increased serum lactate is common but not specific; MRI has some characteristic features, including unilateral temporoparieto-occipital cortex and subcortical patchy T2-FLAIR high signals, restricted dispersion and hyperperfusion of the lesion in the acute phase, and increased peaks of lactate in the brain tissue of the lesion, with an increase in the branches of the middle cerebral artery on the affected side.