Automated Internet of Things (IoT) devices generate a considerable amount of data continuously. However, an IoT network can be vulnerable to botnet attacks, where a group of IoT devices can be infected by malware and form a botnet. Recently, Artificial Intelligence (AI) algorithms have been introduced to detect and resist such botnet attacks in IoT networks. However, most of the existing Deep Learning-based algorithms are designed and implemented in a centralized manner. Therefore, these approaches can be sub-optimal in detecting zero-day botnet attacks against a group of IoT devices. Besides, a centralized AI approach requires sharing of data traces from the IoT devices for training purposes, which jeopardizes user privacy. To tackle these issues in this paper, we propose a federated learning based framework for a zero-day botnet attack detection model, where a new aggregation algorithm for the IoT devices is developed so that a better model aggregation can be achieved without compromising user privacy. Evaluations are conducted on an open dataset, i.e., the N-BaIoT. The evaluation results demonstrate that the proposed learning framework with the new aggregation algorithm outperforms the existing baseline aggregation algorithms in federated learning for zero-day botnet attack detection in IoT networks.