Transcranial photobiomodulation is an innovative method for the stimulation of neural activity which consists of the exposure of neural tissue to low-level light irradiance. In the present study, light-emitting diodes (LEDs) were used as light source due to their practicality and low cost. The objective was to analyze the effects of transcranial photobiomodulation using 945-nm LED in university students with anxiety and depression. Sample was composed of 22 individuals (17–25 years of age) divided into 2 groups of 11. LED group was treated with 945-nm LEDs for 1 min and 25 s (9.35 J/cm2), while in the placebo group, the device was off when placed in contact with the frontal bone for the same amount of time as in treatment group. Participants were evaluated at baseline and after 30 days with the hospital anxiety and depression scale (HADS), the faces test, the designs test, and the grip strength test. On the HADS for anxiety, the mean PAB, PAA, PhAB, and PhAA were 13.89 ± 3.55, 12.82 ± 3.18, 10.75 ± 2.49, and 6.66 ± 2.50 points, respectively. In the HADS for depression, the mean for the PDB group was 13.89 ± 3.55 points, in the PhDB group 12.82 ± 3.18 points, in the PDA group 10.75 ± 2.49 points, and in the PhDA group 6.66 ± 2.50 points. In the PA and PD groups, mean values of 8.0 ± 1.5 and 8.9 ± 1.26 scores were obtained, but did not reach significance; however, between PA and PhD analysis, a significance level of p = 0.0003 was obtained. The 945-nm LED transcranial photobiomodulation improves brain activity and may clinically decrease anxiety and depression.