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Abstract Specification and forecast of ionospheric parameters, such as ionospheric electron density (Ne), have been an important topic in space weather and ionospheric research. Neural networks (NNs) emerge as a powerful modeling tool forNeprediction. However, heavy manual adjustments are time consuming to determine the optimal NN structures. In this work, we propose to use neural architecture search (NAS), an automatic machine learning method, to mitigate this problem. NAS aims to find the optimal network structure through the alternate optimization of the hyperparameters and the corresponding network parameters within a pre‐defined hyperparameter search space. A total of 16‐year data from Millstone Hill incoherent scatter radar (ISR) are used for the NN models. One single‐layer NN (SLNN) model and one deep NN (DNN) model are both trained with NAS, namely SLNN‐NAS and DNN‐NAS, forNeprediction and compared with their manually tuned counterparts (SLNN and DNN) based on previous studies. Our results show that SLNN‐NAS and DNN‐NAS outperformed SLNN and DNN, respectively. These NN predictions ofNedaily variation patterns reveal a 27‐day mid‐latitude topsideNevariation, which cannot be reasonably represented by traditional empirical models developed using monthly averages. DNN‐NAS yields the best prediction accuracy measured by quantitative metrics and rankings of daily pattern prediction, especially with an improvement in mean absolute error more than 10% compared to the SLNN model. The limited improvement of NAS is likely due to the network complexity and the limitation of fully connected NN without the time histories of input parameters.