In this paper, we propose a new iterative hierarchical data augmentation (IHDA) method to fine-tune trained deep neural networks to improve their generalization performance. The IHDA is motivated by three key insights: (1) Deep networks (DNs) are good at learning multi-level representations from data. (2) Performing data augmentation (DA) in the learned feature spaces of DNs can significantly improve their performance. (3) Implementing DA in hard-to-learn regions of a feature space can effectively augment the dataset to improve generalization. Accordingly, the IHDA performs DA in a deep feature space, at level l, by transforming it into a distribution space and synthesizing new samples using the learned distributions for data points that lie in hard-to-classify regions, which is estimated by analyzing the neighborhood characteristics of each data point. The synthesized samples are used to fine-tune the parameters of the subsequent layers. The same procedure is then repeated for the feature space at level l+1. To avoid overfitting, the concept of dropout probability is employed, which is gradually relaxed as the IHDA works towards high-level feature spaces. IHDA provided a state-of-the-art performance on CIFAR-10, CIFAR-100, and ImageNet for several DNs, and beat the performance of existing state-of-the-art DA approaches for the same networks on these datasets. Finally, to demonstrate its domain-agnostic properties, we show the significant improvements that IHDA provided for a deep neural network on a non-image wearable sensor-based activity recognition benchmark.