Fine-tuning the deep convolution neural network (CNN) using a pre-trained model helps transfer knowledge learned from larger datasets to the target task. While the accuracy could be largely improved even when the training dataset is small, the transfer learning outcome is similar with the pre-trained one with closed CNN weights, as the backpropagation here brings less updates to deeper CNN layers. In this work, we propose RIFLE - a simple yet effective strategy that deepens backpropagation in transfer learning settings, through periodically ReInitializing the Fully-connected LayEr with random scratch during the fine-tuning procedure. RIFLE brings significant perturbation to the backpropagation process and leads to deep CNN weights update, while the affects of perturbation can be easily converged throughout the overall learning procedure. The experiments show that the use of RIFLE significantly improves deep transfer learning accuracy on a wide range of datasets, outperforming known tricks for the similar purpose, such as dropout, dropconnect, stochastic depth, and cyclic learning rate, under the same settings with 0.5%-2% higher testing accuracy. Empirical cases and ablation studies further indicate RIFLE brings meaningful updates to deep CNN layers with accuracy improved.