We describe the use of a flow-focusing microfluidic reactor to measure the kinetics of the CdSe-to-Ag2Se nanocrystal cation exchange reaction using micro-X-ray absorption spectroscopy (mu XAS). The small microreactor dimensions facilitate the millisecond mixing of CdSe nanocrystals and Ag+ reactant solutions, and the transposition of the reaction time onto spatial coordinates enables the in situ observation of the millisecond reaction using mu XAS. Selenium K-edge absorption spectra show the progression of CdSe nanocrystals to Ag2Se over the course of 100 ms without the presence of long-lived intermediates. These results, along with supporting stopped-flow absorption experiments, suggest that this nanocrystal cation exchange reaction is highly efficient and provide insight into how the reaction progresses in individual particles. This experiment illustrates the value and potential of in situ microfluidic X-ray synchrotron techniques for detailed studies of the millisecond structural transformations of nanoparticles and other solution-phase reactions in which diffusive mixing initiates changes in local bond structures or oxidation states.