The association between air pollution and infant mortality has been inconsistently reported. A few studies have estimated short-term effects of air pollution on infants’ health. This population-based case–control study aimed to examine the potential effects of air pollution on sudden infant death syndrome (SIDS) in the post-neonatal period in Taiwan during 1997–2002. Each case of infant death was matched with 20 randomly selected sex-matched controls who were born on the same day and were still alive. We obtained 24-h measurements of air pollutants and meteorological factors in each case and control with 1- to 14-day lags from 55 air-quality monitoring stations. After controlling for potential confounders, conditional logistic regression analysis was performed to estimate effects of air pollutants on SIDS (n = 398) and respiratory death (n = 121) among neonates. In single- and multi-pollutant models, we found that 100-ppb increment in carbon monoxide (Odds Ratio = 1.04–1.07) and 10-ppb increment in nitrogen dioxide (Odds Ratio = 1.20–1.35) with 1- to 14-day lags were associated with significant increase in SIDS, although a significant relationship between air pollution and respiratory death was not determined in 1- to 14-day lags. Short-term carbon monoxide and nitrogen dioxide exposure were associated with significant increase in SIDS in the post-neonatal period, with latency estimated within days before death.