Humanitarian organizations should respond to more frequent and diverse disaster situations. They therefore have to adapt their processes to become more effective and efficient. Given the need to quickly react for operations face to these situations, it makes humanitarian logistics even more complex than the logistics of most of the industrial sectors. Under these conditions, the integrated information system and in particular its warehouse management (WMS) module provides a real support to logisticians. Although this type of software is often used and adapted from these of the commercial sector, humanitarian organizations have specificities far from standard modules, and many functionalities have been developed to meet these specific needs. However, defining an adapted strategy of system deployment adapted to a particular situation is not an easy task for practitioners. This study proposes a multi-criteria analysis based method to support the decision making process when defining a WMS deployment strategy in the humanitarian context. The proposed method has been applied to the case of Doctors Without Borders Logistic (MSF Logistics).