Recently, our group showed that additional supplementation of Trolox™ (vitamin E analogue) can significantly enhance the antimicrobial photodynamic effect of the photosensitizer Indocyanine green (ICG). Up to now, the combined effect has not yet been investigated on Enterococcus faecalis in dental root canals. In the present in vitro study, eighty human root canals were inoculated with E. faecalis and subsequently subjected to antimicrobial Photodynamic Therapy (aPDT) using ICG (250, 500, 1000 µg/mL) and near-infrared laser light (NIR, 808 nm, 100 Jcm−2). Trolox™ at concentrations of 6 mM was additionally applied. As a positive control, irrigation with 3% NaOCl was used. After aPDT, root canals were manually enlarged and the collected dentin debris was subjected to microbial culture analysis. Bacterial invasion into the dentinal tubules was verified for a distance of 300 µm. aPDT caused significant suppression of E. faecalis up to a maximum of 2.9 log counts (ICG 250 µg/mL). Additional application of TroloxTM resulted in increased antibacterial activity for aPDT with ICG 500 µg/mL. The efficiency of aPDT was comparable to NaOCl-irrigation inside the dentinal tubules. In conclusion, ICG significantly suppressed E. faecalis. Additional application of TroloxTM showed only minor enhancement. Future studies should also address the effects of TroloxTM on other photodynamic systems.