A durable on-column tunneled frit was developed for use in nanoflow UPLC systems. The frit was tunneled during sol-gel reaction. The tunneled-frit fabrication process is easy and reproducible in terms of back pressure and durability. This design creates low backpressure with high liquid flow, which is suitable for the nanoflowUPLC application. A short packing (2 cm C18 particle) tunneled-frit column was demonstrated to sustain 10,000 psi continuous liquid flow for over one week without any particle leakage or pressure instability. The tunneled-frit was also successfully applied to the fabrication of nanoUPLC trapping and analytical column system. It was demonstrated to have high separation efficiency and sensitivity for the analysis of tryptic peptides as well as improved detection sensitivity for phosphopeptide analysis.