Psychosocial stressors are indicative of challenges associated with the social and environmental conditions an individual is subjected to. In a bid to clearly understand the present gaps in school sanitation, this cross-sectional study aimed to identify the sanitation-related psychosocial stressors experienced by students in a Nigerian peri-urban community and their associated impacts. A three-stage sampling technique was used to select 400 students from 10 schools. The students to toilet ratio were 1,521:0 and 1,510:0 for the public-school boys and girls, respectively, and 74:1 and 70:1 for the private-school boys and girls, respectively. Furthermore, public-school students had a significantly higher average stress level (P < 0.001, η2p = 0.071) and a significantly higher proportion of students experiencing school absenteeism (P < 0.001; odds ratio [OR] = 4.8; 95% confidence interval [CI] = 2.7-8.2), missed classes (P < 0.001; OR = 5.8; CI = 2.8-12.0), long urine/fecal retention time (P < 0.001; OR = 2.9; CI = 1.8-4.7), open defecation practice (P < 0.001; OR = 4.2; CI = 2.5-7.1), and open defecation-related anxiety (P < 0.001; OR = 3.6; CI = 2.0-6.5). Moreover, the inability to practice menstrual hygiene management was significantly associated with student-reported monthly school absence among girls (P < 0.001; OR = 4.5; CI = 2.2-9.4). Overall, over 50% of the respondents had reportedly been subjected to at least 14 of the 17 stressors outlined. The most prevalent stressors identified were concerns about disease contraction, toilet cleanliness, toilet phobia, privacy, and assault/injury during open defecation/urination. In conclusion, results show that the absence of functional sanitation facilities purportedly has a grievous effect on the mental, physical, social, and academic well-being of the students. This was clearly seen among public-school students. Subsequent sanitation interventions need to be targeted at ameliorating identified stressors.