This paper reports a unique GC-on-chip module comprising a monolithically integrated semi-packed micro separation column (μSC) and a highly sensitive micro helium discharge photoionization detector (μDPID). While semi-packed μSC with atomic layer deposited (ALD) alumina as a stationary phase provides high separation performance, the μDPID implemented for the first time in a silicon–glass architecture inherits the desirable features of being universal, non-destructive, low power consumption (1.4 mW), and responsive. The integrated chip is 1.5 cm × 3 cm in size and requires a two-mask fabrication process. Monolithic integration alleviates the need for transfer lines between the column and the detector which improves the performance of the individual components with overall reduced fabrication and implementation costs. The chip is capable of operating under the isothermal as well as temperature and flow programming conditions to achieve rapid chromatographic analysis. The chip performance was investigated with two samples: 1) a multi-analyte gas mixture consisting of eight compounds ranging from 98 °C to 174 °C in boiling point and 2) a mixture containing higher alkanes (C9–C12). Our experiments indicate that the chip is capable of providing rapid chromatographic separation and detection of these compounds (<1 min) through the optimization of flow and temperature programming conditions. The GC-on-chip demonstrated a minimum detection limit of ~10 pg which is on a par with the widely used destructive flame ionization detector (FID).