PURPOSE: Stereoelectroencephalography (sEEG) is increasingly utilized for localization of seizure foci, functional mapping, and neurocognitive research due to its ability to target deep and difficult to reach anatomical locations and to study in vivo brain function with a high signal-to-noise ratio. The research potential of sEEG is constrained by the need for accurate localization of the implanted electrodes in a common template space for group analyses. METHODS: We present an algorithm to automate the grouping of sEEG electrodes by trajectories, labelled by target and insertion point. This algorithm forms the core of a pipeline that fully automates the entire process of electrode localization in standard space, using raw CT and MRI images to produce atlas labelled MNI coordinates. RESULTS: Across 196 trajectories from 20 patients, the pipeline successfully processed 190 trajectories with localizations within 0.25±0.55 mm of the manual annotation by two reviewers. Six electrode trajectories were not directly identified due to metal artifacts and locations were interpolated based on the first and last contact location and the number of contacts in that electrode as listed in the surgical record. CONCLUSION: We introduce our algorithm and pipeline for automatically localizing, grouping, and classifying sEEG electrodes from raw CT and MRI. Our algorithm adds to existing pipelines and toolboxes for electrode localization by automating the manual step of marking and grouping electrodes, thereby expedites the analyses of sEEG data, particularly in large datasets.