When using preoperative tractography intraoperatively, inaccuracies due to brain shift might occur. Intraoperative tractography is rarely performed. Elastic fusion (EF) is a tool developed to compensate for brain shift, gravity, and tissue resection based on intraoperative images. Our hypothesis was that preoperative tractography is accurate and adjustments of tractography by intraoperative magnetic resonance imaging (ioMRI)-based EF (IBEF) compensate for brain shift. Between February 2018 and June 2019, 78 patients underwent eloquent (46 motor, 32 language) glioma resection in our department using intraoperative MRI. Mean distances between the resection cavity and tractography were analyzed and correlated with clinical outcomes. The mean ± standard deviation (range) distance after the application of IBEF was 5.0 ± 2.9 mm (0–10 mm) in patients without surgery-related motor deficits compared with 1.1 ± 1.6 mm (0–5 mm) in patients who showed new permanent surgery-related motor deficits postoperatively (p < 0.001). For language, the distance was 0.7 ± 1.2 mm (0–2 mm) in patients with new permanent deficits compared with 3.1 ± 4.5 mm (0–14 mm) in patients without new permanent surgery-related language deficits (p = 0.541). Preoperative tractography corrected by IBEF for subcortical resection of gliomas is highly accurate. However, at least for such subcortical anatomy, the severity of brain shift was considerably overestimated in the past.