Video lectures are commonly used in online and flipped courses, but students often find it challenging to stay engaged and retain lecture content. The current study examined to what extent the power of electroencephalography (EEG) brain activity in the theta (4-7 Hz), alpha (8-12 Hz) and beta (13-20 Hz) bands can dynamically capture fluctuations of student engagement and retention throughout pre-recorded lectures. EEG activity was recorded from 33 college students throughout four video-based chemistry lectures. In-video probes were used to assess both student engagement and content retention at random moments during the video. Our findings reveal that there are significant fluctuations in self-reported engagement throughout pre-recorded lectures. Further, among the three frequency bands that were tested, only alpha power closely tracked fluctuations in self-reported engagement at the individual student level. In-lecture fluctuations in engagement were associated with content retention, but content retention itself was not well captured by EEG activity in any of the frequency bands that were examined. These findings suggest that the design of video lectures should consider fluctuations in student engagement and potentially incorporate self-reported and physiological indicators of engagement. Future research should further investigate how EEG and other physiological engagement indicators can be used in real time to personalize online instruction.