Multidrug-resistant gram-negative bacilli (MDR-GNB) have emerged globally as a serious threat and with a high case fatality rate (CFR). We performed a case-control study in a Thai neonatal intensive care unit to identify the risk factors for 30-day CFR of GNB sepsis between 1991 and 2017. The CFR was analyzed by Cox's proportional hazards model. For 27 years, the percentage of MDR-GNB from GNB sepsis was 66% (169/257). The medians (interquartile ranges) of gestational age and birth weight of the neonates with GNB sepsis were 33 (29-38) weeks and 1,817 (1,100-2,800) grams, respectively. The 30-day CFRs of the neonates with MDR-GNB and non-MDR-GNB sepsis were 33% (56/169) and 20% (18/88), respectively, (hazard ratio [HR] = 1.74; 95% confidence interval [CI]: 1.03-2.97; p = 0.04). Using Cox's proportional hazards model, nonsurvivors in GNB sepsis were more likely to have septic shock (adjusted HR [aHR] = 6.67; 95% CI: 3.28-13.57; p < 0.001) or no microbiological cure (aHR = 10.65; 95% CI: 4.98-22.76; p < 0.001) than survivors. Neonates suspected of sepsis with septic shock need broad-spectrum empirical antimicrobial therapy until the second successive negative culture, especially in high MDR areas.