MicroRNA (miRNA) based therapy for bone repair has shown promising results for regulating stem cell proliferation and differentiation, an efficient and stable vector for delivery of microRNA delivery is needed. The present study explored the stability and functionality of lyophilized mesoporous silica nanoparticles with core-cone structure and coated with polyethylenimine (MSN-CC-PEI) as a system for delivering Rattus norvegicus (rno)-miRNA-26a-5p into rat marrow mesenchymal cells (rBMSCs) to promote their osteogenic differentiation. We assessed the cellular uptake and transfection efficiency of nanoparticles loaded with labelled miRNA using confocal laser scanning microscopy and flow cytometry, and the cell viability using the MTT assay. The expression levels of osteogenic genes after one and two weeks were analysed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Extracellular matrix deposition and mineralization at 3 weeks were evaluated using Picro Sirius red and Alizarin red staining. We also assessed the performance of the delivery system after long term storage, by freeze drying rno-miRNA-26a-5p@MSN-CC-PEI with 5% trehalose and keeping them at -30 °C for 3 and 6 months. Osteogenic differentiation, matrix deposition, and mineralization were all significantly increased by rno-miRNA-26a-5p. In addition, this enhancement was not significantly altered by lyophilization and storage. Overall, these findings support the concept of MSN-CC-PEI as a delivery system for gene therapy. The complex of rno-miRNA-26a-5p@MSN-CC-PEI could efficiently transfect rBMSCs and enhance their osteogenic differentiation. In addition, the lyophilized complexes remain functional after 6 months of storage.