The meaningful problem of improving crane safety, reliability, and efficiency is extensively studied in the literature and targeted via various model-based control approaches. In recent years, crane data-driven modeling has attracted much attention compared to physics-based models, particularly due to its potential in real-time crane control applications, specifically in model predictive control. This paper proposes grammar-guided genetic programming with sparse regression (G3P-SR) to identify the nonlinear dynamics of an underactuated crane system. G3P-SR uses grammars to bias the search space and produces a fixed number of candidate model terms, while a local search method based on an l0-regularized regression results in a sparse solution, thereby also reducing model complexity as well as reducing the probability of overfitting. Identification is performed on experimental data obtained from a laboratory-scale overhead crane. The proposed method is compared with multi-gene genetic programming (MGGP), NARX neural network, and Takagi-Sugeno fuzzy (TSF) ARX models in terms of model complexity, prediction accuracy, and sensitivity. The G3P-SR algorithm evolved a model with a maximum mean square error (MSE) of crane velocity and sway prediction of 1.1860 × 10−4 and 4.8531 × 10−4, respectively, in simulations for different testing data sets, showing better accuracy than the TSF ARX and MGGP models. Only the NARX neural network model with velocity and sway maximum MSEs of 1.4595 × 10−4 and 4.8571 × 10−4 achieves a similar accuracy or an even better one in some testing scenarios, but at the cost of increasing the total number of parameters to be estimated by over 300% and the number of output lags compared to the G3P-SR model. Moreover, the G3P-SR model is proven to be notably less sensitive, exhibiting the least deviation from the nominal trajectory for deviations in the payload mass by approximately a factor of 10.