Socio-economically advantaged students often pursue more demanding and prestigious educational paths than their less advantaged peers, even at similar performance levels. These “secondary effects” of socio-economic status (SES) are typically studied in the context of school continuation decisions or track choice but may also be present in school choice. In highly stratified systems with limited direct influence on track placement, advantaged parents may seek alternative strategies, such as school choice, to enhance their children’s educational opportunities. This study examines secondary effects in secondary school choice in the Netherlands, focusing on track offerings (single-track versus multi-track schools) and ability grouping practices (homogeneous versus heterogeneous classes). Moreover, it investigates the role of social capital – resources embedded in peer and parental networks in primary school – in these patterns. I use unique (linked) full-population register data (N_students = 328,334), peer nomination data in primary schools (N_students = 2,468), and novel web data on school characteristics (N_schools = 1,165) for Dutch students who recently transitioned to secondary school. Hypotheses are tested through regression analyses with a fixed effects estimator to account for selection into primary schools. Findings reveal stratification in secondary school choice. Higher SES students tend to avoid schools only offering pre-vocational education (and no general tracks), prefer schools only offering pre-university education (and no lower tracks), and tend to choose schools with heterogeneous ability classes at intermediate performance levels. There is no strong evidence for the relation between social capital and the type of school chosen. A notable exception is that lower SES students are more likely to avoid pre-vocational schools when integrated into resource-rich parental networks. This suggests that such networks may play a compensatory role, steering students away from decisions that may impede upward track mobility.