Since the use of light and electronic devices is inevitable, the use of blue light filters (in various light sources, electronic devices or optical devices including intraocular lenses) has been shown to improve sleep quality, especially in later hours of the day and during night time. In this study, we examine the effect of the blue light on sleep and wakefulness rhythms and positive and negative emotions. This randomized clinical trial was conducted with 80 AJA University of Medical Sciences employees who use computers at least 2 h a day. All subjects were employees of the discharge unit of Imam Reza Hospital, which is located next to AJA University. The subjects were divided into two groups of 40 people, blue light filter software intervention and sham treatment. Pittsburgh Sleep Quality Index (PSQI), Positive and Negative Affect Schedule (PANAS), Visual Function Questionnaire (VFQ), Epworth Sleepiness Scale (ESS) and salivary melatonin and cortisol levels were assessed for both groups before and 3 months after the intervention. Data analysis was performed using IBM SPSS statistics for windows, version 21.0 (Armonk, NY: IBM Corporation). P value ≤ 0.05 was considered as statistically significant. The results showed that the Pittsburgh sleep scale after the intervention was significantly lower in the intervention group than in the control group. After the intervention, the VFQ was significantly lower in the intervention group than in the control group (P = 0.018). There was no significant difference in the Epworth Sleepiness Scale (ESS) between the two study groups after the intervention (P = 0.370). There was no significant difference in Positive and Negative Affect Schedule (PANAS) in the two study groups after the intervention (P = 0.140). After the intervention, cortisol levels were significantly higher in the intervention group than in the control group (P = 0.006). Also, the amount of cortisol increased significantly in the intervention group (P = 0.028). The amount of melatonin decreased significantly in the intervention group (P = 0.034). The sleep quality score after the intervention was significantly lower in the intervention group than in the control group. This indicates better sleep quality in the intervention group. The results also show that the level of visual fatigue in the intervention group decreased significantly. However, no significant change was detected regarding positive and negative emotions. After the intervention, cortisol levels were significantly higher in the intervention group than the control group. In addition, cortisol levels increased significantly and melatonin levels decreased significantly in the intervention group during the course of study.