Botnet detection is a critical step in stopping the spread of botnets and preventing malicious activities. However, reliable detection is still a challenging task, due to a wide variety of botnets involving ever-increasing types of devices and attack vectors. Recent approaches employing machine learning (ML) showed improved performance than earlier ones, but these ML- based approaches still have significant limitations. For example, most ML approaches can not incorporate sequential pattern analysis techniques key to detect some classes of botnets. Another common shortcoming of ML-based approaches is the need to retrain neural networks in order to detect the evolving botnets; however, the training process is time-consuming and requires significant efforts to label the training data. For fast-evolving botnets, it might take too long to create sufficient training samples before the botnets have changed again. To address these challenges, we propose a novel botnet detection method, built upon Recurrent Variational Autoencoder (RVAE) that effectively captures sequential characteristics of botnet activities. In the experiment, this semi-supervised learning method achieves better detection accuracy than similar learning methods, especially on hard to detect classes. Additionally, we devise a transfer learning framework to learn from a well-curated source data set and transfer the knowledge to a target problem domain not seen before. Tests show that the true-positive rate (TPR) with transfer learning is higher than the RVAE semi-supervised learning method trained using the target data set (91.8% vs. 68.3%).