Bioluminescent dinoflagellates emit light when exposed to shear stresses above a certain threshold. Studying how flow can trigger individual cell flashes and observing their kinetics can help us understand how bioluminescent flashes occur in nature. We devised a unique millifluidics apparatus essentially composed of a syringe pump and a glass capillary where dinoflagellate cells are injected. The first bioluminescent flash of cells was captured using a camera. Flashes were tracked from the onset of the first visible emission of light to the last, and integrated densities of flashes were obtained for every frame of the video. Living cells were counted downstream in a second glass capillary using a 405 nm laser and a camera capturing red fluorescent flashes from chlorophyll, and counter-verified by microscope counts. We modelled the velocity and shear stress cells experienced in the system from the dimensions and measured flow rates using ANSYS Fluent. The cells reached a maximum average shear stress of 0.5 N/m2, five times the reported shear threshold for Pyrocystis fusiformis. We observed the typical “first flash” waveform, consistent with what had been measured with other methods, and roughly ten times more intense than the following flashes for P. fusiformis. Our results indicate that a higher level of shear stress could produce a higher flash intensity. The proportion of cells flashing increased with higher shear stress within the studied range. Our method also allowed us to observe the flow-stimulated kinetics of the first flash to study the photoinhibition of bioluminescence in Pyrocystis fusiformis.