This study analyses the alignment between Estonia’s public transport (PT) network and functional regions derived from daily commuting related travel. The aim of the research is to analyse whether public transport services provide sufficient levels of access to local commuting centres based on openly available GTFS data and functional regions defined from commuting statistics. The analysis across 21 functional regions reveals that while PT services cover nearly the entire country, alignment with designated commuting centres is considerably lower. 365 localities (44.5%) have their primary PT destination aligned with their designated commuting centre. 566 localities (69.1%) meet the minimum level of daily access to their commuting centre defined as at least one morning peak connection to the centre and one evening peak return. Population-weighted analysis shows that 12.4% of residents outside commuting centres do not have sufficient PT access to their centre for daily commuting. Travel times to the commuting centre are long, with the median PT journey time from localities with direct connections being 43 minutes. The results reveal the misalignment between commuting-based functional regions and PT provision organised in respect to administrative units, indicating priorities for better integrating PT planning with commuting patterns.