This paper presents the effect of shallow trench isolation (STI) on the dark count rate (DCR) and after-pulsing probability (APP) of deep-junction-based single-photon avalanche diodes (SPADs). Two different SPADs were fabricated in 110 nm CMOS image sensor technology, one with STI and the other without STI between its anode and cathode. With TCAD simulations and measurements, we have clearly demonstrated that the SPAD without STI enables a dramatic decrease in DCR by more than three orders of magnitude without suffering from the lateral leakage current between the anode and cathode. By excluding the STI from the device, the proposed SPAD also achieves a negligible APP while the SPAD with STI shows a very high APP of 92%. Thanks to the low-noise performance, the proposed SPAD becomes operable with higher excess bias voltage so that it achieves good photon detection probability, 58.3% at 500 nm and 3% at 940 nm, and timing jitter, 71 ps full width at half maximum at 670 nm, when the reverse bias voltage is 17 V.