Background: Previous studies have provided evidence of inequalities in the coverage of COVID-19 vaccination. However, evidence of such inequalities in delays in vaccinations is lacking. Our study examined the socioeconomic and geographic disparities in terms of days to get the first and second dose of COVID-19 vaccinations in Indonesia. Methods: We conducted a cross-sectional study using the WhatsApp messaging app and social media platforms during December 2021–February 2022. We distributed the questionnaire through our university network to reach all regions. We included 3592 adults aged 15+ years in our analysis. We used two main dependent variables: days to receive the first dose (after national vaccine rollout) and days to receive the second dose (after receiving the first dose). We examined a range of socioeconomic and geographic indicators, including education level, income level, formal employment, working in health facilities, being a health worker, and region. We controlled for sex, age, religion, and urbanicity. We performed multivariate logistic regressions in STATA 15. Results: Our findings show considerable delays in getting the first dose among participants (160.7 days or about 5.4 months on average) from Indonesia’s national COVID-19 vaccination rollout on 13 January 2021. However, we found a shorter period to receive the second dose after receiving the first dose (41.1 days on average). Moreover, we found significant socioeconomic (i.e., education, income, formal employment, working in health facilities, and being a health worker) and geographic (i.e., in and out of the Java region) inequalities in terms of delays in getting the first dose. However, we did not find significant inequalities in getting the second dose for most inequality indicators, except for working in health facilities. By region, we found that participants living in more deprived areas (out of the Java region) received the second dose 4.9 days earlier. One of the study’s key limitations is that there may be an inherent bias with respect to socioeconomics factors since it was conducted online (web-based). Conclusions: While there were considerable delays in getting the first dose, especially among those of a lower socioeconomic status and those in more deprived areas, the waiting time for the second dose was relatively similar for everyone once they were in the system. Effective efforts to address inequalities are essential to ensuring the effectiveness of the national COVID-19 vaccination rollout.