Electromagnetic induction (EMI) is used widely for environmental studies. The apparent electrical conductivity (EC_a), which can be mapped efficiently with EMI, correlates with a variety of important soil attributes. EMI instruments exist with several configurations of coil spacing, position, and height. There are general, rule-of-thumb guides to choose an optimal instrument configuration for a specific survey. The goal of this study was to use machine learning to improve this design optimization task. In this investigation, we used machine learning as an efficient tool for interpolating among the results of many forward model runs. Specifically, we generated an ensemble of 100,000 EMI forward models representing the responses of many EMI configurations to a range of three-layer subsurface models. We split the results into training and testing subsets and trained a decision tree (DT) with gradient boosting (GB) to predict the subsurface properties (layer thicknesses and EC values). We further examined the value of prior knowledge that could limit the ranges of some of the soil model parameters. We made use of the intrinsic feature importance measures of machine learning algorithms to identify optimal EMI designs for specific targets. The optimal designs identified using this approach agreed with those that are generally recognized as optimal by informed experts for standard targets, giving confidence in the ML-based approach. The approach also offered insight that would be difficult if not impossible to offer based on rule-of-thumb optimization. We contend that such ML-informed design approaches could be applied broadly to other survey design challenges.