Nucleic acid extraction from clinical specimens is essential for accurate molecular diagnostic assays. However, conventional extraction methods are often slow, equipment-dependent, and require trained personnel, limiting the point-of-care applicability. We introduce a novel silica-based pipet tip column that enables rapid nucleic acid extraction from clinical samples in less than 3 min. The pipet tip column has a large surface area for effective nucleic acid extraction using chaotropic salts. The integrated disposable 1 mL syringe eliminates the need for a pipet. Sample application is achieved by simply pushing and pulling the syringe, requiring no external power or specialized equipment. The pipet tip column performance was validated using standard influenza A and B, severe acute respiratory syndrome coronavirus-2, and Staphylococcus aureus samples, achieving high performance even at low concentrations (1 PFU/mL or 1 TCID/mL). Our approach demonstrated a 90-110% nucleic acid recovery rate, comparable to that of traditional methods. Pipette tip-column nucleic acid extraction was successful for nasopharyngeal and saliva samples, including those in loop-mediated isothermal amplification assays. The pipet tip column provides a rapid, cost-effective, reliable, and portable solution for on-site molecular diagnostics. Additionally, nonexpert users can perform nucleic acid extraction without sample transportation or storage, reducing contamination risks and operational costs.