In 2009, the FDA required a black box warning (BBW) on bupropion and varenicline, the two commonly prescribed smoking cessation agents due to reports of adverse neuropsychiatric events. We investigated if there was a decline in use of bupropion and varenicline after the BBW by comparing the percent using these medications before and after BBW. We conducted a retrospective observational study using data from the Medical Expenditure Panel Survey from 2007 to 2014. The study sample consisted of adult smokers, who were advised by their physicians to quit smoking. We divided the time period into “pre-warning”, “post-warning: immediate”, and “post-warning: late.” Unadjusted analysis using chi-square tests and adjusted analyses using logistic regressions were conducted to evaluate the change in bupropion and varenicline use before and after the BBW. Secondary analyses using piecewise regression were also conducted. On an average, 49.04% of smokers were advised by their physicians to quit smoking. We observed a statistically significant decline in varenicline use from 22.1% in year 2007 to 9.23% in 2014 (p value < 0.001). In the logistic (Adjusted Odds Ratio = 0.36, 95% CI = 0.22–0.58) and piecewise regressions (Odds Ratio = 0.64, 95% CI = 0.41–0.99) smokers who were advised to quit smoking by their physicians were less likely to use varenicline in the immediate post-BBW period as compared to pre-BBW period. While the use of varenicline continued to be significantly low in the late post-BBW period (AOR = 0.45, 95% CI = 0.31–0.64) as compared to the pre-BBW period, the trend in use as seen in piecewise regression remained stable (OR = 0.90, 95% CI = 0.75–1.06).