The seismic fragility of reinforced concrete (RC) frame systems considering the disadvantages of both structural eccentricities and pulse-like earthquake effects is investigated. A total of 24,000 nonlinear time history analyses are performed using CANNY program. The influence of pulse-like ground motion and strength eccentricity on the seismic fragility is studied quantitatively, in terms of interstorey drift, ductility, and floor rotation. The results show that the probability of reaching and exceeding a predefined damage state (P f) is apparently higher for pulse-like case than for non-pulse-like case. At a moderate eccentricity level of 0.2 and a moderate damage state (selected moderate case) with a peak ground acceleration (PGA) of 0.4 g, the P f values of interstorey drift and ductility for pulse-like case are 14 and 10% larger, respectively, than those for non-pulse-like case. The strength eccentricity also has a great effect on the structural seismic fragility. The PGA at a given probability level decreases with increasing eccentricity. For the selected moderate case, the PGAs at an exceeding probability of 50% are 0.40, 0.56, and 1.15 g for the P f values of interstorey drift, ductility, and floor rotation, respectively. The obtained fragility curves could help to quantitatively evaluate the seismic behavior of eccentric RC frame structures subjected to pulse-like ground motions.