Systems and methods for intelligent fan identification are described. In some embodiments, an Information Handling System (IHS) may include: an embedded controller (EC); and a memory coupled to the EC, the memory having program instructions stored thereon that, upon execution by the EC, cause the IHS to: detect a cooling fan configuration issue; determine that a number of cooling fans in the IHS has not changed between a previous configuration and a current configuration; and in response to the determination, abstain from identifying the cooling fan configuration issue as a cooling fan error.