There have been various tests to evaluate the physical capabilities and body kinetics of seafarers. This study evaluated the Functional Capacity Evaluation (FCE), which has been part of the pre-employment medical exam (PEME) for Filipino seafarers since 2008. A total of 33,616 Filipino seafarers in cargo merchant ships underwent PEMEs at our clinic from January 2009 to December 2011. We divided these into groups where one group underwent the FCE during their PEME (FCE group n=5578) and another group that did not (non-FCE group n= 28,038). The medical repatriation rates from for these groups were monitored from January 2009 to June 2012. The medical repatriation for low back injury cases and rates of this group were evaluated and compared to the FCE group. Results showed that there were significantly less low back injuries as the cause for medical repatriations in the FCE group as compared to the low back injuries of the non-FCE group with relative risk of 0.346. This study has shown that the FCE has been significant in decreasing the number of repatriations secondary to back pain in seafarers. Thus, it is recommended that the FCE be made a regular component of the PEME.