There is evidence that smoking-cessation success differs by menstrual phase and sex hormone levels; however, the biological mechanisms underlying these differences are not clear. One possibility is that variation in cortisol throughout the menstrual cycle and early smoking abstinence may be partly responsible. The goal of this secondary-data analysis was to conduct a within-subject examination of the effects of menstrual phase and smoking abstinence on salivary cortisol and mood. Data are from a controlled crossover trial, in which participants completed 2 testing weeks during their follicular and luteal phases. During each testing week, they smoked ad libitum during the first 2 days and then abstained from smoking during the next 4 days. Salivary cortisol and self-reported mood were collected 5 times on the day before abstinence (D0) and the first (D1) and third (D3) days of abstinence. Participants (n = 125) were, on average (mean ± SE), 29.4 ± 0.6 years old and smoked 12.6 ± 0.5 cigarettes/day. Whereas salivary cortisol varied significantly by time of day (p < .0001) and smoking abstinence (D0 to D1: β = −0.06 ± 0.02 log[ng/ml], p = .0074 and D3: β = −0.05 ± 0.02 log[ng/ml], p = .0117). no significant differences by menstrual phase were observed. Craving increased from D0 to D1 during the follicular phase but decreased in the luteal phase (+0.31 vs. −0.15, β = 0.46 ± 0.19, p = .0162). This work builds on prior observations in demonstrating a decrease in cortisol in acute smoking abstinence and menstrual phase differences in craving. The results provide further evidence that cortisol levels do not vary by menstrual phase in the first few days of abstinence.