Background: High-definition transcranial direct current stimulation (HD-tDCS) holds promise for therapeutic use in psychiatric disorders. One obstacle for the implementation into clinical practice is response variability. One way to tackle this obstacle is the use of Individualized head models. Objective: This study investigated the variability of HD-tDCS induced electric fields (EFs) and its impact on resting-state functional connectivity (rsFC) during different time windows. Methods: In this randomized, double-blind, and sham controlled study, seventy healthy males underwent 20 min of 1.5 mA HD-tDCS on the right inferior frontal gyrus (rIFG) while undergoing resting-state functional magnetic resonance imaging (rs-fMRI). Individual head models and EF simulations were created from anatomical images. The effects of HD-tDCS on rsFC were assessed using a seed-to-voxel analysis. A subgroup analysis explored the relationship between EF magnitude and rsFC during different stimulation time windows. Results: Results highlighted significant variability in HD-tDCS-induced EFs. Compared to the sham group, the active group showed increased rsFC between the rIFG and the left prefrontal cortex, during and after stimulation. During active stimulation, EF magnitude correlated positively with rsFC between the rIFG and the left hippocampus initially, and negatively during the subsequent period. Conclusion: This study indicated an HD-tDCS induced increase of rsFC between left and right prefrontal areas. Furthermore, an interaction between the magnitude and the duration of HD-tDCS on rsFC was observed. Due to the high EF variability that was apparent, these findings highlight the need for individualized HD-tDCS protocols and the creation of head models to optimize effects and reduce response heterogeneity.