Dentinal tubule penetration influences root canal treatment sealing. The aim of this study was to compare dentinal penetration of two clinical presentations of silicate-based sealers using confocal laser. Sixty single-rooted human teeth from 50–70 year-old patients extracted for orthodontic/periodontal reasons were used. Canals were prepared using Mtwo system up to 35/0.04, with 5.25% NaOCl irrigation and final irrigation using 17% EDTA. Teeth were randomly assigned into study groups (n_i = 20): EndoSequence BC sealer (ES, group 1), BioRoot RCS (BR, group 2); and a control group (n_c = 20) with AH Plus (AHP). Root canals were obturated with 35/0.04 gutta-percha (single-cone technique). The samples were obtained from apical, middle, and coronal thirds. Dentinal tubule penetration depth and percentage of penetration around the canal perimeter were measured. The statistical analysis was performed using Mann Whitney U test and Wilcoxon t-test (95% confidence interval). ES exhibited a significantly higher penetration than AHP in apical and middle thirds (p < 0.05), and in middle and coronal thirds relative to BR (p < 0.05). The percentage of penetration around the canal perimeter was significantly higher for ES compared to BR in all thirds, but only in the apical third for AHP (p < 0.05). The pre-mixed silicate-based sealer exhibited better penetration than the powder/liquid one.