This study investigated electroencephalogram (EEG) changes during movement preparation and execution in stroke patients. EEG-based event-related potential (ERP) technology was used to measure brain activity changes. Seventeen stroke patients participated in this study and completed ERP tests that were designed to measure EEG changes during unilateral upper limb movements in preparation and execution stages, with Instruction Response Movement (IRM) and Cued Instruction Response Movement (CIRM) paradigms. EEG data were analyzed using motor potential (MP) in the time domain and the mu-rhythm and beta frequency band response mean value (R-means) in the time–frequency domain. In IRM, the MP amplitude at Cz was higher during hemiplegic arm movement than during unaffected arm movement. MP latency was shorter at Cz and the contralesional motor cortex during hemiplegic arm movement in CIRM compared to IRM. No significant differences were found in R-means among locations, between movement sides in both ERP tests. This study presents the brain activity changes in the time and time–frequency domains in stroke patients during movement preparation and execution and supports the contralesional compensation and adjacent-region compensation mechanism of post-stroke brain reconstruction. These findings may contribute to future rehabilitation research about neuroplasticity and technology development such as the brain–computer interface.