An apparatus and method are provided for performing scheduling in a Node B for data transmission of a user equipment (UE) in a mobile communication system supporting an enhanced uplink dedicated channel (E-DCH). The Node B receives, from a radio network controller (RNC), scheduling assistance information for an uplink service to be provided from the UE. The Node B estimates a data amount for the uplink service on the basis of the scheduling assistance information in each scheduling period. The Node B schedules data transmission for the uplink service according to the estimated data amount.