Comparative studies of human–dog cognition have grown exponentially since the 2000’s, but the focus on how dogs look at us (as well as other dogs) as social partners is a more recent phenomenon despite its importance to human–dog interactions. Here, we briefly summarise the current state of research in visual perception of emotion cues in dogs and why this area is important; we then critically review its most commonly used methods, by discussing conceptual and methodological challenges and associated limitations in depth; finally, we suggest some possible solutions and recommend best practice for future research. Typically, most studies in this field have concentrated on facial emotional cues, with full body information rarely considered. There are many challenges in the way studies are conceptually designed (e.g., use of non-naturalistic stimuli) and the way researchers incorporate biases (e.g., anthropomorphism) into experimental designs, which may lead to problematic conclusions. However, technological and scientific advances offer the opportunity to gather much more valid, objective, and systematic data in this rapidly expanding field of study. Solving conceptual and methodological challenges in the field of emotion perception research in dogs will not only be beneficial in improving research in dog–human interactions, but also within the comparative psychology area, in which dogs are an important model species to study evolutionary processes.