Site characterization is one of the most important components in seismic hazard analysis because it accounts for the important effects of near‐surface geology on ground motion. It is usually quantified based on the time‐averaged S‐wave velocity () for the top 30 m of the profile (). In this study, we estimate the site class in Jakarta based on structure estimated using microtremor array observations. The results show that microtremor‐derived profiles agree well with standard penetration test‐derived profiles at nine sites. The site‐class estimates in the Jakarta area can be divided into two National Earthquake Hazards Reduction Program classes: (a) site class E (soft soil) located in alluvium, beach ridge, and alluvial fan deposits in northern and western Jakarta, and (b) site class D (stiff soil) found mainly in alluvial fan deposits in southeastern Jakarta. The variation of in Jakarta leads to different soil amplification factors that will impact the seismic hazard at the surface. We show that the seismic hazard resulting from selected ground‐motion models (GMMs) illustrates a clear influence of site effects at long periods (). However, the effect on peak ground acceleration and response spectra for short periods (0.2 s) appear to be less pronounced, due to the GMMs’ treatment of basin effects and nonlinear soil behavior. Available GMMs may not accurately account for such effects in the Jakarta basin, and GMMs specific to Indonesia should be developed to accurately assess seismic hazard there.