Dynamic Voltage and Frequency Scaling (DVFS) on General-Purpose Graphics Processing Units (GPGPUs) is now becoming one of the most significant techniques to balance computational performance and energy consumption. However, there are still few fast and accurate models for predicting GPU kernel execution time under different core and memory frequency settings, which is important to determine the best frequency configuration for energy saving. Accordingly, a novel GPGPU performance estimation model with both core and memory frequency scaling is herein proposed. We design a cross-benchmarking suite, which simulates kernels with a wide range of instruction distributions. The synthetic kernels generated by this suite can be used for model pre-training or as supplementary training samples. Then we apply two different machine learning algorithms, Support Vector Regression (SVR) and Gradient Boosting Decision Tree (GBDT), to study the correlation between kernel performance counters and kernel performance. The models trained only with our cross-benchmarking suite achieve satisfying accuracy (16%∼22% mean absolute error) on 24 unseen real application kernels. Validated on three modern GPUs with a wide frequency scaling range, by using a collection of 24 real application kernels, the proposed model is able to achieve accurate results (5.1%, 2.8%, 6.5% mean absolute error) for the target GPUs (GTX 980, Titan X Pascal and Tesla P100).