We study the windowed Fourier transform in the framework of Clifford analysis, which we call the Clifford windowed Fourier transform (CWFT). Based on the spectral representation of the Clifford Fourier transform (CFT), we derive several important properties such as shift, modulation, reconstruction formula, orthogonality relation, isometry, and reproducing kernel. We also present an example to show the differences between the classical windowed Fourier transform (WFT) and the CWFT. Finally, as an application we establish a Heisenberg type uncertainty principle for the CWFT.