In electric vehicles (EVs), battery management systems (BMS) carry out various functions for effective utilization of stored energy in lithium-ion batteries (LIBs). Among numerous functions performed by the BMS, estimating the state of health (SOH) is an essential and challenging task to be accomplished at regular intervals. Accurate estimation of SOH ensures battery reliability by computing remaining lifetime and forecasting its failure conditions to avoid battery risk. Accurate estimation of SOH is challenging, due to uncertain operating conditions of EVs and complex non-linear electrochemical characteristics demonstrated by LIBs. In most of the existing studies, standard charge/discharge patterns with numerous assumptions are considered to accelerate the battery ageing process. However, such patterns and assumptions fail to reflect the real world operating condition of EV batteries, which is not appropriate for BMS of EVs. In contrast, this research work proposes a unique SOH estimation approach, using an independently recurrent neural network (IndRNN) in a more realistic manner by adopting the dynamic load profile condition of EVs. This research work illustrates a deep learning-based data-driven approach to estimate SOH by analyzing their historical data collected from LIBs. The IndRNN is adapted due to its ability to capture complex non-linear characteristics of batteries by eliminating the gradient problem and allowing the neural network to learn long-term dependencies among the capacity degradations. Experimental results indicate that the IndRNN based model is able to predict a battery’s SOH accurately with root mean square error (RMSE) reduced to 1.33% and mean absolute error (MAE) reduced to 1.14%. The maximum error (MAX) produced by IndRNN throughout the testing process is 2.5943% which is well below the acceptable SOH error range of ±5% for EVs. In addition, to demonstrate effectiveness of the IndRNN attained results are compared with other well-known recurrent neural network (RNN) architectures such as long short-term memory (LSTM) and gated recurrent unit (GRU). From the comparison of results, it is clearly evident that IndRNN outperformed other RNN architectures with the highest SOH accuracy rate.