Background: Students who fail to complete high school, on average, have less earnings, pay fewer taxes, and require increased government expenditures compared to those who do reach this milestone. Especially in urban jurisdictions, this can lead to reduced municipal fiscal health. Alternative high schools have been one intervention employed to improve the outcomes of students who have previously dropped out. Also, in recent decades, early warning indicator (EWI) systems have been put in place to flag students who are at risk for not completing school. However, the current EWI metrics for student attendance are insufficient for the population that attends alternative high schools. Methods: Administrative data were obtained from an alternative charter high school in a large urban city in the northeast United States (n = 224). Logistic regression analyses were conducted to test the utility of traditional EWI operationalizations of student attendance against more targeted measures, with student graduation serving as a dichotomous outcome variable. Results: Of the models tested, the model that flagged student non-attendance as missing consecutive days three or more times during the first 12 weeks of school had the greatest explanatory power (McFadden’s R2 = 0.301) and best overall model fit. Conclusions: Traditional definitions of attendance are less useful in schools doing re-engagement work, and more targeted indicators serve as more effective EWIs in these settings.