Multiple detailed mechanisms have been proposed to describe GPCR-mediated intracellular calcium oscillations and have been formulated as mathematical models. Here we describe phase-locking analysis, a qualitative test that can be used to evaluate those models. Phase-locking refers to the phenomenon whereby an oscillatory system synchronizes to a periodic input. In our experiments, single cells are subjected to square-wave pulses of ligand in a microfluidic device and calcium is imaged using the FRET probe YC3.60. Comparison of cell responses with model predictions gives insights into relevant biological mechanisms. We anticipate that phase-locking analysis will be useful in evaluating GPCR as well as other signalling pathways.