We investigate social inequalities based on social background in the choice of the academic track among equally performing students, and how indicators derived from the rational choice framework contribute to account for such inequalities. We discuss the main theoretical concepts underpinning rational choice theory as applied to educational decisions: perceived costs, benefits, and risks of failure; relative risk aversion; and time-discounting preferences. In the empirical section, we use a unique dataset concerning the transition to different tracks in upper secondary school in a large Southern Italian region. By using various regression methods and the Karlson/Holm/Breen decomposition technique, we show that social inequalities in access to the academic track are considerable, even in recent cohorts, and that they are largely not explained by previous academic performance. Indicators linked to key concepts proposed by the rational choice theory—as measured in this study—account, as a whole, for 31% of the gap based on parental education, and for 40% of the gap based on parental occupation. The most important sources of inequalities among those this study examines are the expected benefits associated with the educational alternatives and the time-discounting preferences, while relative risk aversion and the perceived chances of success play negligible roles.