Bokeh is used for finance, management, big data mining, graphing business patterns, web applications such as weather data and renewable energy forecasts, viewing energy production data, disaster resource management, displaying agricultural sensor data online, analysis of data from industrial machinery (wind turbines, trains, power plants), and mapping clinical trials using AERO plots, among many other uses.

Astronomers at the Space Telescope Science Institute in Baltimore have been developing a suite of Bokeh server web apps to help figure out what it can do for their particular science aims. These tools also help STSI astronomers communicate with journalists, aerospace industry leaders, and members of Congress about the science of their mission.

It is also used by computational biologists working to identify biomolecular markers that predict the therapeutic response of cancer patients, since Bokeh provides a framework for creating multiple interactive plots that can be linked to shared data sources (i.e. gene expression data).