Purification of bacteria from human blood samples is essential for rapid identification of pathogens by molecular methods, enabling faster and more accurate diagnosis of bloodstream infection than conventional gold standard blood culture methods. The inertial microfluidic method has been broadly studied to isolate biological cells of interest in various biomedical applications due to its label-free and high-throughput advantages. However, because of the bacteria's tininess, which ranges from 0.5 μm to 3 μm, they are challenging to be effectively focused and sorted out in existing inertial microfluidic devices that work well with biological cells larger than 10 μm. Efforts have been made to sort bacterial cells by utilizing extremely small channel dimensions or employing a sheath flow, which thus results in limitations on the throughput and ease of operation. To overcome this challenge, we develop a method that integrates a non-Newtonian fluid with a novel channel design to allow bacteria to be successfully sorted from larger blood cells in a channel dimension of 120 μm × 20 μm without the use of sheath flows. The throughput of this device with four parallel channels is above 400 μL per minute. The real-time polymerase chain reaction (qPCR) analysis indicates that our inertial sorting approach has a nearly 3-fold improvement in pathogen recovery compared with the commonly used lysis-centrifugation method at pathogen abundances as low as 10² cfu mL⁻¹. With the rapid and simple purification and enrichment of bacterial pathogens, the present inertial sorting method exhibits an ability to enhance the fast and accurate molecular diagnosis of bloodstream bacterial infection.