The development of the process and scale-up of the agitated column was carried out by the knowledge and prediction of mass transfer rates. This study aimed to apply and validate the mass transfer models for measuring the mass transfer rate. Experimental studies were performed in a pilot-scale agitated column with sieve structure, with cerium extraction from the aqueous phase to the organic phase. The extraction rate with concentration profile was measured and used as an input to mass balance expressions to calculate the mass transfer coefficients. The results showed that the axial dispersion and backflow parameters also change significantly under operating conditions. The most influential parameter was agitation speed; increasing it from 170 to 410 rpm, the extraction efficiency, backflow parameters and axial dispersion parameters were shifted from 50%, 0.5 and 0.5–90%, 3 and 6, respectively. The evaluation of mass transfer models indicates that cerium removal improves when the forward mixing model with drop size distribution (X-AARE, Y-AARE equals 7.68, and 8.66) is used instead of PFM, BFM, and ADM models. This work illustrates the possibility of predicting the mass transfer performance of a pilot-scale agitated column using a validated FMM model for extraction of rare-earth ions.