Disclosed are systems, methods and computer program products for configuring application control rules. The system creates a new application control rule that specifies restrictions or permission on execution a software application, a function of an application or a category of applications. The system then collects information about one or more computers in a network, including information about software applications deployed on the computers and existing application control rules. The system then tests the new application control rule using the collected information to determine verdicts rendered by the new application control rule that restrict or permit execution of an application, certain function of an application or a category of applications. The system then compares verdicts rendered by the new application rule with the verdicts rendered by the existing application control rules to identify conflicting rules, and reconfigures the new application control rule to eliminate conflicts.