This paper reports a comprehensive comparison for mortality and technique failure rates between automated peritoneal dialysis (APD) and continuous ambulatory peritoneal dialysis (CAPD) in Taiwan. A propensity-score matched cohort study was conducted by retrieving APD and CAPD patients identified from the Taiwan National Health Insurance Research Database between 2001 and 2010. The main outcomes were the 5-year mortality and technique failure rates. Further analyses were then carried out based upon the first (2001–2004), second (2005–2007), and third (2008–2010) sub-periods. Similar baseline characteristics were identified for APD (n = 2,287) and CAPD (n = 2,287) patients. The proportion on APD therapy increased rapidly in the second sub-period. As compared to CAPD patients of this sub-period, APD patients had a significantly higher risk of mortality (HR, 1.37; 95% CI 1.09–1.72; p < 0.01) and technique failure (HR, 1.43; 95% CI, 1.10–1.86; p < 0.01), particularly in the first year after peritoneal dialysis commencement. However, APD patients had similar mortality and technique failure rates to those of CAPD patients throughout the full sample period and the first and third sub-periods. These findings do not suggest the presence of a clear advantage of CAPD over APD. Differences observed between these two modalities might be attributed to specials circumstances of sub-periods.