Quantification of total belowground carbon (C) input and allocation to various pools in rice–soil systems depending on plant age, chase period, and nitrogen (N) availability. Rice plants with and without N fertilization were 13CO2 pulse labelled at tillering, elongation, heading, and filling stages and were destructively sampled after 6 h of labelling and at the final harvest. The allocation of C by rice was also generalized based on literature pertaining to 94 studies with respect to plant age and chase period. The C allocation in roots and soil strongly decreased with plant age. The literature review showed that C allocation to roots increased within the first 10 days of labelling and remained stable thereafter. Nitrogen fertilization had no effect on C allocation immediately after assimilation, but increased C remained belowground at 1.7-times that at final harvest. The total belowground net C input by one rice crop was 630–1080 kg C ha−1, including rhizodeposition of 160–330 kg C ha−1. Multiple pulse labelling at various plant growth stages and taking multiple subsequent samples as well as nutrient availability should be considered for tracing C flows more accurately for precise C balance in rice paddy systems.