The disruption of in-person schooling during the Covid-19 pandemic has affected students’ learning, development, and well-being. Students in Latin America and the Caribbean have been hit particularly hard because schools in the region have stayed closed for longer than anywhere else, with long-term expected adverse consequences. Little is known about which factors are associated with the slow in-person return to school in the region and how these factors have had differential effects based on students’ socio-economic status. Combining a longitudinal national survey of the Chilean school system and administrative datasets, we study the supply and demand factors associated with students’ resuming in-person instruction and the socio-economic gaps in school reopening in Chile in 2021. We defined socio-economic status based on parents’ education and household income. Our results show that in-person learning in 2021 was limited mainly by supply factors (i.e., sanitary, administrative, and infrastructure restrictions). However, once the supply restrictions decreased, many low-income students and their families did not resume in-person instruction. We found vast inequalities in face-to-face instruction by school’s socio-economic characteristics. On average, schools in the highest 10% of the socio-economic distribution had three times higher attendance rates than the remaining 90%. We found no significant differences between schools in the lowest 90% of the distribution. After exceptionally long school closures, most school authorities, students, and their families did not return to in-person instruction, particularly those of low socio-economic status. These inequalities in in-person instruction will expand existing disparities in students’ learning and educational opportunities.