The present disclosure relates to a method, apparatus and system for processing a configuration update failure, belonging to the field of communications. The method includes: setting a times threshold for receiving an eNB configuration update failure message; sending an eNB configuration update message to an MME or a neighboring eNB after configuration information is updated; receiving, from the MME or the neighboring eNB, an eNB configuration update failure message including a Time-To-Wait IE; calculating the times for receiving the eNB configuration update failure message; comparing the calculated times for receiving the eNB configuration update failure message with the set times threshold to determine whether the calculated times exceed the set times threshold; and stopping sending the eNB configuration update message if the calculated times exceed the set times threshold. The apparatus includes: a first sending module, a first receiving module, a first counting module, a first threshold setting module, a first comparing module and a first notifying module. The present disclosure can relieve the load of the system and improve the robustness and stability of the system.