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Abstract Whooping cough also called Pertussis is a highly contagious respiratory infection that affects all age populations. Given recent pertussis outbreaks, there is an urgent need for a point-of-care (POC) device for rapid diagnosis of pertussis. Herein, we report a low-cost microfluidic POC device integrated with loop-mediated isothermal amplification (LAMP) technique for the rapid and accurate diagnosis of pertussis. The 3D-printed bioanalyzer housed not only the biochip but also an in-house-developed portable and fully battery-powered heater for rapid POC detection of pertussis, without the need of external electricity. The fluorescence-based results could be rapidly visualized in about one hour by the naked eye without the need for any additional instrumentation. In addition, a simple centrifuge-free sample preparation process was optimized for the efficient lysis of pertussis samples and successfully used for direct detection of bacteria in nasopharyngeal samples. High sensitivity, with a limit of detection (LOD) of 5 DNA copies per LAMP zone, and high specificity were demonstrated. We envision that the microfluidic POC device can be used in various venues such as medical clinics, schools, and other low-resource settings for the fast detection of pertussis. Graphical abstract We report a low-cost microfluidic point-of-care (POC) platform integrated with loop-mediated isothermal amplification (LAMP) supported by a portable battery-powered heater for rapid and instrument-free detection of whooping cough in resource-limited settings. Image 1 Highlights • We for the first time report a low-cost hybrid microfluidic platform integrated with LAMP for rapid and instrument-free detection of whooping cough (pertussis). • We developed a portable and fully battery-powered heater to support on-chip LAMP reactions, which significantly enhanced the capacity for point-of-care detection without the requirement of the external AC power supply. • The microfluidic approach demonstrated high specificity by detecting B. pertussis and other Bordetella species. The limit of detection of 5 DNA copies per LAMP zone was achieved, demonstrating high detection sensitivity. • By using an optimized centrifuge-free lysis protocol, direct detection of B. pertussis bacteria was achieved. • Our novel microfluidic approach has great potential for point-of-care detection of many other pathogens such as foodborne pathogens, especially for low-resource settings. [ABSTRACT FROM AUTHOR]