This study aimed to describe the fabrication of a novel dental composite by surface modification of silica fillers with polyether ether ketone (PEEK) and assess surface coverage of fillers and the effect of different concentration of modified fillers on degree of conversion, flexural strength, polymerization shrinkage, water sorption and solubility, viscosity and thermal expansion of the formulated composites. In this experimental study, aminosilane derivative of PEEK was synthesized and grafted to the silica filler surface, then evaluated using a fourier transform infrared spectroscopy (FTIR), and thermo-gravimetric analysis (TGA). Silica-PEEK fillers were then mixed with Bis-GMA/TEGDMA resin base in 10, 30, and 50 wt%. The most relevant physico-chemical properties were evaluated and compared with a control composite resin group containing conventional 3-(methacryloxypropyl) trimethoxysilane (γ-MPS) modified fillers. Data were analyzed by ANOVA and Tukey’s HSD test. (α = 5%). The experimental composite with 30% modified fillers showed highest flexural strength and degree of conversion (DC) ( p < 0.05), and comparable polymerization shrinkage and viscosity to the control composites ( p > 0.05). After thermocycling, the composite with 30% modified fillers showed the lowest solubility and water sorption ( p < 0.05). Surface modification of silica fillers with PEEK polymer significantly increases the resistance of the filler–matrix interface to hydrolysis. The above mentioned intervention can improve mechanical properties of the composite and may be considered as a promising protocol to reduce the failure of dental composites.