The aim of this study was to investigate and compare the influence of zirconium dioxide nanoparticles (ZrO2 NPs) and silicon dioxide nanoparticles (SiO2 NPs) addition and printing orientation on the flexural strength (FS) of provisional three-dimensional (3D) printing resins undergoing thermal cycling (TC). Three dimensional-printed resin (NextDent C&B MFH) was used to fabricate 300bar-shaped specimens (25×2×2mm3 ). The ZrO2 NPs and SiO2 NPs specimens were divided into two groups, then subdivided into three groups, based on the nanoparticle concentration (i.e., 0 wt% (original group), 0.5 wt%, and 1 wt%). Each concentration was printed in three printing orientations (0°, 45°, and 90°). The printed specimens were exposed to 5000 cycles of TC, followed by a three-point bending test to assess the FS. Fracture surface analysis was conducted by using a scanning electron microscope (SEM). For data analysis, ANOVA and Tukey's post hoc were utilized (α = 0.05). Compared to the original material, the addition of ZrO2 NPs and SiO2 NPs had a significantly positive impact on the FS, (P > 0.001). After TC, the FS of the original group decreased significantly and had the lowest value. The highest FS value was observed in 1% ZrO2 NPs at 0°. Regardless of the nanoparticle concentration, the 0° orientation consistently showed a higher FS, compared to the 45° and 90° orientations. At all orientations (i.e., 0°, 45°, and 90°), the FS significantly increased with the addition of NPs, compared with that of the original material (P > 0.001). TC had a significantly negative effect on the FS of the unmodified groups. However, no significant differences existed in FS among the modified groups after TC. The addition of SiO2 NPs and ZrO2 NPs increased the FS of the 3D-printed provisional resin. Regardless of the nanoparticle concentration, the 0° orientation had the higher FS. TC had an effect on the original resin, whereas it had no significant effect on the nanoparticle-modified resins. In clinical practice, 3D-printed provisional nanocomposite resins printed at the 0° orientation could be recommended for long-term dental provisional restorations.