A multi-rate sample MRI (magnetic resonance imaging) digital receiver maintains synchronization of digitally processed signals. This multi-rate sample data system is used to demodulate and filter a digitized MRI RF signal. A phase/timing relationship is established between the signal received and processed by the digital receiver, and the physical nuclear magnetic resonance (NMR) process the body being imaged is undergoing. Once established, the phase/timing relationship is maintained for the duration of the particular NMR experiment being performed. Special logic in the digital system ensures that the data output is synchronized with an external synchronous signal controlling data acquisition within the MRI system. Optimum signal processing is performed to minimize the time between the end of the acquisition control signal and the last output from the digital signal processing system.