Many studies have shown the benefits of augmented reality (AR) to improve manufacturing and control processes in industry. However, the presentation of AR content through optical see-through head-mounted displays may induce unnatural viewing conditions, which consequences on the user’s visual system have not been investigated yet. This study aimed at assessing whether using AR instructions to guide a manual task, i.e., conditions where the user is forced to repeatedly look at and accommodate in different planes to extract information from both real and virtual environments, could potentially impact the visual system of operators. A before/after design study was carried out, asking 26 participants to perform Lego assemblies for 30 min with either paper or AR instructions. The effects of using AR compared to paper instructions were evaluated both on binocular vision, with classical optometric measurements, and on visual fatigue, with the Virtual Reality Symptoms Questionnaire. No clinically significant differences in optometric measurements (far/near visual acuity, stereoacuity, phoria, convergence, fusional amplitude, accommodation amplitude, accommodative convergence) have been found between AR and paper instructions, and only negligible fatigue symptoms have been seen specifically for AR. Results from both objective and subjective measurements suggest that there is no impact of AR on the oculomotor system and that, in this specific case of use, AR can be safely used for production operators.