Warehouse Management System (WMS) is a new paradigm on integrating a set of business processes. The primary goal of WMS is to efficiently control all activities in an organization. However, most of existing WMSs focus mainly on data input, data processing, and report generation. Recent researches attempt to make use of results from the field of intelligent system in parts of the business processes within WMSs. This paper proposes new alternative to WMS. It is called intelligent WMS (i-WMS). This system consists of five subsystems: intelligent logistic system, intelligent warehouse system, real-time transportation monitoring, intelligent sales forecasting system, and intelligent executive summary system. The reported research in this paper integrates state-of-the-art results in the field of intelligent systems—neural network, bee colony optimization, fuzzy control, and decision support system—together with the latest technologies—RFID and Android-based handheld devices—in every part of business processes in WMS.