We used an offline tracer transport model, driven by reanalysis ocean currents and coupled to a simple biogeochemical model, to synthesize the surface ocean pCO2 and air–sea CO2 flux of the global ocean from 1996 to 2004, using a variational assimilation method. This oceanic CO2 flux analysis system was developed at the National Institute for Environmental Studies (NIES), Japan, as part of a project that provides prior fluxes for atmospheric inversions using CO2 measurements made from an on-board instrument attached to the Greenhouse gas Observing SATellite (GOSAT). Nearly 250 000 pCO2 observations from the database of Takahashi et al. (2007) have been assimilated into the model with a strong constraint provide by ship-track observations while maintaining a weak constraint of 20% on global averages of monthly mean pCO2 in regions where observations are limited. The synthesized global air–sea CO2 flux shows a net sink of 1.48 PgC yr−1. The Southern Ocean air–sea CO2 flux is a sink of 0.41 PgC yr−1. The interannual variability of synthesized CO2 flux from the El Niño region suggests a weaker source (by an amplitude of 0.4 PgC yr−1) during the El Niño events in 1997/1998 and 2003/2004. The assimilated air–sea CO2 flux shows remarkable correlations with the CO2 fluxes obtained from atmospheric inversions on interannual time-scales.