Student attendance in American public schools is a critical factor in securing limited operational funding. Student and teacher attendance influence academic performance. Limited data exist on indoor air and environmental quality (IEQ) in schools, and how IEQ affects attendance, health, or performance. This study explored the association of student absence with measures of indoor minus outdoor carbon dioxide concentration (dCO2). Absence and dCO2 data were collected from 409 traditional and 25 portable classrooms from 22 schools located in six school districts in the states of Washington and Idaho. Study classrooms had individual heating, ventilation, and air conditioning (HVAC) systems, except two classrooms without mechanical ventilation. Classroom attributes, student attendance and school-level ethnicity, gender, and socioeconomic status (SES) were included in multivariate modeling. Forty-five percent of classrooms studied had short-term indoor CO2 concentrations above 1000 parts-per-million (ppm). A 1000 ppm increase in dCO2 was associated (p < 0.05) with a 0.5% to 0.9% decrease in annual average daily attendance (ADA), corresponding to a relative 10% to 20% increase in student absence. Annual ADA was 2% higher (p < 0.0001) in traditional than in portable classrooms.