The structure and variability of the Ryukyu Current System (RCS), which forms the western boundary current along the eastern slope of the Ryukyu Islands, are studied using results from a 32-layer, 1/12.5° global HYbrid Coordinate Ocean Model (HYCOM) and Navy Coupled Ocean Data Assimilation (NCODA) reanalysis for the period 1993-2012. It is confirmed that the reanalysis realistically reproduces salient features of the observed currents at three sections southeast of Miyakojima, Okinawa and Amami-Ohshima. The mean velocity sections show well-developed subsurface velocity maxima between 700 and 900 m. The current core southeast of Amami-Ohshima shows year-to-year variations with cyclonic (anticyclonic) circulation east of Amami-Ohshima generating weak (strong) velocity cores. Interaction of the RCS with an anticyclonic eddy often produces a two-core velocity structure, with a surface core in the upper 300 m and a deeper core near 700-900 m. The horizontal structure of the RCS at 15 m depth shows a well-developed northeastward current northeast of Okinawa, which is partly fed by the southwestward extension of the anticyclonic recirculation gyre. The RCS forms a continuous northeastward current from Miyakojima to Amami-Ohshima below 500 m with shoreward intensification. The circulation at 2000 m shows a seasonal flow reversal, which is northeastward from December to June and southwestward from August to October with July and November being the transition months. The volume transports across these three sections have respective mean values of 0.6, 6.2 and 12.4 Sv (1 Sv ≡ 106 m3 s-1) and standard deviations of 10.2, 7.1 and 11.3 Sv. They have dominant seasonal variations with the maximum in winter and spring and the minimum in summer. The interannual variation of the transport anomaly, which co-varies with the RCS core, results from westward propagating mesoscale eddies arriving from the Pacific interior.