The aim of this study was to compare the associations between indicators of energy intake and expenditure with excess weight and obesity in women who work full-time in sedentary and less sedentary jobs. Data were from 3444 participants the Australian Longitudinal Study on Women's Health, who reported their weight, dietary intake, physical activity and occupation in 2009 (baseline), and weight in 2012 (follow-up). Participants were categorised as being in a ‘less sedentary’ or ‘sedentary’ job, based on occupational activity patterns. Odds of excess weight (BMI ≥ 25) at baseline and of being obese (BMI ≥ 30) at follow-up, by indicators of energy intake and expenditure, were compared in the two occupational groups. In multivariate analyses, high non-work sitting time and saturated fat intake were associated with increased odds of obesity at 3-year follow-up in both occupational groups. In the sedentary job group, high physical activity (in leisure and transport) was associated with a 51% reduction in odds of obesity (OR 0.49, 95%CI 0.25–0.97). In the less-sedentary job group, energy intake and high soft drink consumption were associated with markedly increased odds of obesity (OR 1.67 95%CI 1.07–2.61; OR 2.08 95%CI1.42–3.05, respectively). In this cohort of young Australian women, sedentariness at work did not markedly affect the prevalence of excess weight or obesity. Indicators of high energy intake and low energy expenditure were associated with increased odds of both excess weight and obesity, regardless of sedentariness of occupational group.