In this study, clinoptilolite (CLN) was employed as a reinforcement in a polymer-based composite scaffold in bone tissue engineering and evaluated in vivo for the first time. Highly porous, mechanically stable, and osteogenic CLN/PCL-PEG-PCL (CLN/PCEC) scaffolds were fabricated with modified particulate leaching/compression molding technique with varying CLN contents. We hypothesized that CLN reinforcement in a composite scaffold will improve bone regeneration and promote repair. Therefore, the scaffolds were analyzed for compressive strength, biodegradation, biocompatibility, and induction of osteogenic differentiation in vitro. CLN inclusion in PC-10 (10% w/w) and PC-20 (20% w/w) scaffolds revealed 54.7% and 53.4% porosity, higher dry (0.62 and 0.76 MPa), and wet (0.37 and 0.45 MPa) compressive strength, greater cellular adhesion, alkaline phosphatase activity (2.20 and 2.82 mg/g(DNA)/min), and intracellular calcium concentration (122.44 and 243.24 g Ca/mg(DNA)). The scaffolds were evaluated in a unicortical bone defect at anterior aspect of proximal tibia of adult rabbits 4 and 8 weeks postimplantation. Similar to in vitro results, CLN-containing scaffolds led to efficient regeneration of bone in a dose-dependent manner. PC-20 demonstrated highest quality of bone union, cortex development, and bone-scaffold interaction at the defect site. Therefore, higher CLN content in PC-20 permitted robust remodeling whereas pure PCEC (PC-0) scaffolds displayed fibrous tissue formation. Consequently, CLN was proven to be a potent reinforcement in terms of promoting mechanical, physical, and biological properties of polymer-based scaffolds in a more economical, easy-to-handle, and reproducible approach.