Smoking prevalence remains high among individuals who are homeless, partly due to stressors related to homelessness. Beyond housing insecurity, homelessness involves financial stresses and unmet subsistence needs. In particular, food insecurity contributes to negative health outcomes and other health risks. This study examined associations between food insecurity severity and smoking among homeless and marginally housed women in San Francisco, California. We used data from 247 women from a longitudinal cohort study. Generalized estimating equations were used to estimate longitudinal associations between study factors and smoking based on data from five biannual assessment points between 2009 and 2012. The longitudinal adjusted odds of smoking were higher among severely food insecure individuals compared to those who were not food insecure (AOR = 1.68, 95% CI [1.02, 2.78]), while associations with other study factors, including demographics, time, HIV status, mental health, and substance use (except marijuana use), did not reach levels of significance. Similar adjusted longitudinal results were observed when food insecurity was the dependent variable and smoking an independent variable, suggesting the possibility of a bidirectional association. Considering unmet needs, such as food and hunger, may improve comprehensive smoking cessation strategies targeting individuals for whom mainstream tobacco control efforts have not been effective. Similarly, offering improved access to smoking cessation resources should be considered in efforts to address food insecurity among individuals experiencing homelessness.