Point-of-care (POC) pathogen detection is highly desirable in diverse fields such as infectious disease diagnosis, food safety testing, and environmental monitoring. Herein, the study seeks to address this critical need by developing an automated microfluidic photothermal quantitative polymerase chain reaction (AMP-qPCR) system in a greatly simplified format. A key element of AMP-qPCR is an architecture that combines the design of a clockwork-like, magnetically-driven multi-chamber cartridge with the use of a cheap black tape beneath the PCR chamber as a fast photothermal-responsive engine. This not only enables the unprocessed sample to be lysed, purified, and subjected to real-time fluorescence PCR in an ultracompact and autonomous manner but also eliminates the need for sophisticated photonic material/device fabrication that is frequently required for performing ultrafast photothermal PCR. It is shown that AMP-qPCR can accomplish high-efficient bacterial DNA extraction and quantitative PCR within 18.5 min, enabling accurate quantification of bacteria concentration from 10⁸ to 10² CFU·mL⁻¹. Furthermore, its practical applicability is demonstrated in detecting Neisseria gonorrhoeae from sexually transmitted infection-suspected patients by using clinical urine and cervical swab specimens, exhibiting matched performance to the benchtop automated machine. The presented platform enhances the availability of POC molecular diagnostics for on-site and in-home testing.