Background: The Apgar score of newborn babies is a determining factor involved with mortality of newborns after birth. Regarding the disagreement on advantages and possible disadvantages of propofol and thiopental in the available references, the study was triggered with the aim of analyzing effects of two mentioned drugs on babies’ Apgar score. Methods: In this double-blind clinical trial, a total of 100 healthy women who volunteered to undertake cesarean operation were selected and then divided randomly into two equal groups using statistical blocking. One group was treated by propofol while other one was treated by thiopental. The prescribed drugs for both groups were identical. Babies’ Apgar score 1 and 5 minutes after birth and recovery period and some of the critical maternal parameters after operation were recorded. The obtained data were analyzed by SPSS 19 software. Results: Apgar score I minute 1 (p=0.317) and Apgar score in minute 5 (p=1.00) for propofol group were not different meaningfully. The groups had significant differences in the indices such as first systolic (P=0.00) and diastolic (P=0.00) pressure in recovery, last diastolic pressure in recovery (P=0.001) and duration of postoperative recovery (P=0.001). Statistical analysis of nausea and vomit in both groups showed that they are lower in propofol group rather than the thiopental group (p=0.000). Conclusion: Propofol and thiopental did not differ significantly in Apgar score, but it seems that propofol can be a better option to induce anesthesia for an elective cesarean operation.