Multiple reviews point out that immersive virtual reality (IVR) educational studies often lack the consideration of learning theories in research design and IVR application development to promote students' learning. In response to the lack of theoretical foundations in educational research of IVR applications, an increased number of scholarly studies have been published in recent years to incorporate learning theories into the design of VR applications, research, and lesson design of IVR-based lessons, particularly in the field of science education. Through synthesizing IVR educational research articles that used learning theories, this review aims to study how to best design IVR instructions using learning theories as foundations. Supported by various learning design theories, the synthesis of the reviewed studies (n = 29) reveals that students' learning outcomes could be enhanced by (1) providing students with high level of control over their IVR learning experiences, (2) minimizing cognitive loads imposed by IVR, (3) integrating learners' characteristics into IVR learning application design, and (4) adding reflective tasks before or after IVR applications. Details of these theoretically informed lesson design were also explored. Based on these findings, we propose six design principles to help facilitate the transition to IVR lessons and improve IVR learning application design and lesson design. This set of design principles will provide theoretically informed pedagogical suggestions for future educators.