Background: In the new Sustainable Development Goal 4, quality of education defined as equity and inclusion alongside traditional learning outcomes, has replaced the narrow goal of access to primary education stipulated in the Millennium Development Goal 2. Since 2000, considerable progress has been made towards improving access to school for children in India, yet questions remain regarding not just children with disabilities’ access and acquisition of basic learning skills, but also completion of learning cycles. Methods and findings: Between November, 2, 2011 and June 20th 2012, we interviewed 1294 households about activity limitations and functioning difficulties associated with a health problem among all family members using a validated screening instruments, as well as questions about access, retention and barriers to education. We found that vulnerable children, particularly children with disabilities are less likely to start school and more likely to drop out of school earlier and before completing their high school education than non-disabled children, showing that the learning process is not inclusive in practice. The gap is wider for girls, economically deprived children, or children from households where the head is uneducated. Conclusions: Firstly, in order to fill the existing knowledge gap on education of children with disabilities in line with SDG4, not only is there a necessity for relevant data with regards to learning outcomes, but also an urgent requirement for more innovative information pertaining to relational aspects of learning that reflect inclusion. Secondly, a stronger understanding of the implications of early assessment would further promote equity in education. Finally, research should tackle learning as a complex and dynamic phenomenon. Education needs to fulfil its instrumental value, but must also re-claim its intrinsic value that often gets watered down in the journey from policies to implementation.