Resting state functional MRI (rs-fMRI) is an imaging technique that allows the spontaneous activity of the brain to be measured. Measures of functional connectivity highly depend on the quality of the BOLD signal data processing. In this study, our aim was to study the influence of preprocessing steps and their order of application on small-world topology and their efficiency in resting state fMRI data analysis using graph theory. We applied the most standard preprocessing steps: slice-timing, realign, smoothing, filtering, and the tCompCor method. In particular, we were interested in how preprocessing can retain the small-world economic properties and how to maximize the local and global efficiency of a network while minimizing the cost. Tests that we conducted in 54 healthy subjects showed that the choice and ordering of preprocessing steps impacted the graph measures. We found that the csr (where we applied realignment, smoothing, and tCompCor as a final step) and the scr (where we applied realignment, tCompCor and smoothing as a final step) strategies had the highest mean values of global efficiency (eg) . Furthermore, we found that the fscr strategy (where we applied realignment, tCompCor, smoothing, and filtering as a final step), had the highest mean local efficiency (el) values. These results confirm that the graph theory measures of functional connectivity depend on the ordering of the processing steps, with the best results being obtained using smoothing and tCompCor as the final steps for global efficiency with additional filtering for local efficiency.