An online system of the underground neutrino detector, Super-Kamiokande is scheduled to be upgraded in 2008 together with front-end electronics. This detector consists of 50 000 tons of pure water equipped with about 13 000 photo-multipliers (PMTs) to detect Cherenkov light. The new online system is required to accept the dataflow of up to 800 MB/s from the front-end electronics and process them for the offline analysis. We will utilize a Gigabit Ethernet network and parallel data processing to handle this large amount of flow. In the new data acquisition scheme, we will not use a hardware event-trigger but read out every hit data from the front-end electronics and process them by the online farm. Therefore, there is no threshold of the number of PMT hits and the detector will become more sensitive to important cosmic-ray events such as relic neutrino from supernova and low energy solar neutrino. In addition to that, a dead-timeless system is desirable for the continuous measurement 365 days a year. In this paper, the detailed design of the upgraded online system and testing activities using prototypes will be described.