In the pursuit of accurate experimental and computational data while minimizing effort, there is a constant need for high-fidelity results. However, achieving such results often requires significant computational resources. To address this challenge, this paper proposes a deep operator learning-based framework that requires a limited high-fidelity dataset for training. We introduce a novel physics-guided, bi-fidelity, Fourier-featured deep operator network (DeepONet) framework that effectively combines low- and high-fidelity datasets, leveraging the strengths of each. In our methodology, we begin by designing a physics-guided Fourier-featured DeepONet, drawing inspiration from the intrinsic physical behavior of the target solution. Subsequently, we train this network to primarily learn the low-fidelity solution, utilizing an extensive dataset. This process ensures a comprehensive grasp of the foundational solution patterns. Following this foundational learning, the low-fidelity deep operator network’s output is enhanced using a physics-guided Fourier-featured residual deep operator network. This network refines the initial low-fidelity output, achieving the high-fidelity solution by employing a small high-fidelity dataset for training. Notably, in our framework, we employ the Fourier feature network as the trunk network for the DeepONets, given its proficiency in capturing and learning the oscillatory nature of the target solution with high precision. We validate our approach using a well-known 2D benchmark cylinder problem, which aims to predict the time trajectories of lift and drag coefficients. The results highlight that the physics-guided Fourier-featured deep operator network, serving as a foundational building block of our framework, possesses superior predictive capability for the lift and drag coefficients compared to its data-driven counterparts. The bi-fidelity learning framework, built upon the physics-guided Fourier-featured deep operator, accurately forecasts the time trajectories of lift and drag coefficients. A thorough evaluation of the proposed bi-fidelity framework confirms that our approach closely matches the high-fidelity solution, with an error rate under 2%. This confirms the effectiveness and reliability of our framework, particularly given the limited high-fidelity dataset used during training.