Background: Cognitive impairments in bipolar disorder (BD) such as memory deficits are associated with poor functional outcomes and it has been suggested that the brain-derived neurotrophic factor (BDNF) Val66Met polymorphism contributes to individual variability in memory function in BD. The current study investigated the relationship between the BDNF Val66Met polymorphism, neural activity during a picture-encoding task, and subsequent memory recall. Methods: A total of 70 patients with BD grouped according to genotype [ValVal or Met carriers (MetVal/MetMet)] underwent fMRI while performing a picture-encoding task. Memory for the encoded pictures was tested with a subsequent free recall memory task. Results: There was no difference between the ValVal homozygotes and Met carriers in the involvement of hypothesized memory encoding regions i.e. hippocampus and dorsal prefrontal cortex (dPFC). However, an exploratory whole-brain analysis showed greater encoding-related lateral occipital cortex activity in Met carriers. Behaviorally, Met carriers also showed better free recall of the encoded pictures. Conclusions: We found no effect of the BDNF genotype on encoding-related hippocampal and dPFC activity in BD, although Met carriers showed superior memory performance after the scan, which could be related to more efficient perceptual processing during encoding.