Brian Gunning made many contributions to the study of structure–function relationships in plant cells using light and electron microscope techniques in conjunction with physiological correlates. His early work was on plastids, especially the geometry of prolamellar body membranes. With John Pate, he named and established the significance of transfer cells and their widespread roles in providing short-range, high-intensity translocation pathways for solutes in plant tissues. He studied another transport system in plants, the intercellular connections known as plasmodesmata, and co-authored the first full textbook about them.

His later work concerned the nature and roles of microtubules in plant morphogenesis, focusing on the miniature root of the water fern Azolla as a model system, which he characterised in great detail. He also pioneered methods for following cell cycle transitions in microtubule arrays in other tissues using confocal microscopy and immunofluorescent labelling. In retirement, Brian compiled a comprehensive and widely used atlas of micrographs and live-cell movies entitled Plant Cell Biology on DVD — Information for Students and a Resource for Teachers.