Background: High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data. Results: We developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and “paint” pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point. Conclusion: NetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.