Background <p>Socio-economic status is a known predictor of childhood obesity. Improvements to school meals have been promoted as a method of combating rising childhood obesity rates, especially in low-income populations. However, little is known about how school food offerings differ across areas of low and high socio-economic status. This study aims to examine differences in school lunch nutrition across socioeconomic strata and compare these differences to small-scale regional childhood obesity prevalence.</p> Methods <p>This was a cross-sectional study of electronically published school lunch menus and a longitudinal analysis of UK National Child Measurement Programme data. Participants were a randomly selected sample of free, state-funded primary schools with 200–399 pupils within the two highest and two lowest child-poverty boroughs of Inner London, UK (<i>n</i> = 20), along with borough-level data on child BMI in reception and year 6 (<i>n</i> = 4). School meals were evaluated for nutrient content using Nutritics and for objective healthiness using the Nutrient Profiling Model.</p> Results <p>Lunches in high-poverty boroughs were significantly lower in total energy, carbohydrates, fat, and sugars (<i>p</i> &lt; 0.001), but lower in iron, zinc, and Vitamin A (<i>p</i> &lt; 0.01) compared with the most affluent areas. Using the nutrient profiling model, meals in high-poverty boroughs scored significantly better in both main courses (mean difference = -0.53, <i>p</i> = 0.016) and desserts (mean difference = 5.50, <i>p</i> &lt; 0.001).</p> Conclusions <p>Overall, meals in high-poverty boroughs were more nutritious than those in the most affluent areas, though they were lower in some key micronutrients. Despite this, rates of overweight, obesity, and severe obesity are higher in these boroughs, indicating that factors other than school food nutrition may play more crucial roles in the relationship between socio-economic status and childhood obesity.</p>