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Children orphaned by HIV/AIDS (“AIDS orphans”) suffer numerous early-life adverse events which have a long-lasting effect on brain function. Although previous studies found altered electroencephalography (EEG) oscillation during resting state in children orphaned by HIV/AIDS, data are limited regarding the alterations in connectivity and microstate. The current study aimed to investigate the functional connectivity (FC) and microstate in children orphaned by HIV/AIDS with resting-state EEG data. Data were recorded from 63 children orphaned by HIV/AIDS and 65 non-orphan controls during a close-eyes resting state. The differences in phase-locking value (PLV) of global average FC and temporal dynamics of microstate were compared between groups. For functional connectivity, children orphaned by HIV/AIDS showed decreased connectivity in alpha, beta, theta, and delta band compared with non-orphan controls. For microstate, EEG results demonstrated that children orphaned by HIV/AIDS show increased duration and coverage of microstate C, decreased occurrence and coverage of microstate B, and decreased occurrence of microstate D than non-orphan controls. These findings suggest that the microstate and functional connectivity has altered in children orphaned by HIV/AIDS compared with non-orphan controls and provide additional evidence that early life stress (ELS) would alter the structure and function of the brain and increase the risk of psychiatric disorders.