Recently, the concept of the microgrid (MG) has been developed to assist the penetration of large numbers of distributed energy resources (DERs) into distribution networks. However, the integration of DERs in the form of MGs disturbs the operating codes of traditional distribution networks. Consequently, traditional protection strategies cannot be applied to MG against short-circuit faults. This paper presents a novel intelligent protection strategy (NIPS) for MGs based on empirical wavelet transform (EWT) and long short-term memory (LSTM) networks. In the proposed NIPS, firstly, the three-phase current signals measured by protective relays are decomposed into empirical modes (EMs). Then, various statistical features are extracted from the obtained EMs. Afterwards, the extracted features along with the three-phase current measurement are input to three different LSTM network to obtain exact fault type, phase, and location information. Finally, a trip signal based on the obtained fault information is generated to disconnect the faulty portion from the rest of the MG. The significant feature of the proposed NIPS is that it does not need adaptive relaying and communication networks. Moreover, it is independent of the operating scenario and hence fault current magnitude. To evaluate the efficacy of the proposed NIPS, exhaustive simulations are performed on an international electro-technical commission (IEC) MG. The simulation results confirm the efficiency of the proposed NIPs in terms of accuracy, dependability, and security. Moreover, comparisons with existing intelligent protection schemes validate that the proposed NIPS is highly accurate, secure, and dependable.