The Wireless sensor networks (WSNs) getting especially designed auto configured networks to sense and transmit the data from constituent deployed sensor nodes to base station. These networks are immensely prone to a variety of faults. This work puts forward an Energy Efficient Fault Tolerant Multipath Routing (EEFTMR) scheme. The elite group-based routing scheme has been employed for routing the sensor nodes and cluster head selection. A fault tolerant cluster head node is going to get selected to improve the fault tolerance of the cluster heads. This fault tolerant cluster head node enables monitoring of cluster head performance and temporary storage of cluster head data until the successful data transmission. A chart was drawn and the hypothesis-based testing was employed in cluster head node to identify the faulty sensor node. In addition, a multipath scheme was adopted for fault tolerant data transmission based on an overall resultant performance parameter derived from residual energy, hop count, network reliability and data speed. The simulation results showcase the superiority of the proposed scheme with respect to network delay (73.7%), energy efficiency (9.6%), network lifetime (9%) and fault free data throughput (61.3%) in comparison of existing elite group-based routing scheme.