Monitoring system is a crucial part in establishing sophisticated IT infrastructure. Monitoring of IT infrastructure becomes indispensable for knowing the status and performance of technology components. Complex infrastructure, such as virtualization and cloud computing systems, boost up the number of nodes to be monitored. Notifications accumulate, which makes it more difficult to track problems. With lots of unneccessary notifications, the challenge to provide availability and improve service quality becomes more complex. A monitoring system that can deliver accurate monitoring information is needed. This research proposed a method to manage IT infrastructure monitoring system using Lean method. Lean method is a popular method of process management and has been successfully used in several IT process improvement projects. The results of this research show that lean methods can be applied to increase the quality of monitoring system, through the process stages that have been described in the lean implementation principle. Quantitatively it is known that after the lean method is applied, the number of network elements, nodes and interfaces monitored increases by 39%, 105% and 1%, respectively. While the alerts and events generated decreased by 77% and 49%, respectively. Qualitatively based on the identification of value achievement, the system can deliver the value expected by the customer, in which case the customer is a user of monitoring system.