The paucity of information on the number of accessible sanitation facilities in secondary schools in developing countries has hindered efforts in attaining sustainable development in this area. Therefore, this study was designed to bridge that gap. The cross-sectional study utilized a 4-stage sampling technique to select 386 students from schools in Badagry, Lagos. Pre-tested questionnaire and observational checklists were used to obtain data. Data were analyzed using descriptive statistics and logistic regression at 5% level of significance. Respondents’ mean age was 15.8±1.5 years and 55.2% were female. On-site observation revealed that all the schools had improved sanitation facilities, while 37% of the available toilet compartments were inaccessible to the students. Majority (85%) of the facilities provided limited service, while 15% provided basic service. The student to toilet ratio for the public school girls and boys were 3191: 1 and 642: 1 respectively, while the private school had a ratio of 257: 1 and 289: 1 for girls and boys respectively. Some of the sanitation practices observed in the schools were open defecation (35.4%), toilet avoidance (21%), and prolonged urine and feacal retention (57.4%). Students from the public school were about 3 times more likely to practice open defecation (OR= 2.87; CI= 1.160-7.095). Also, male students were more likely to practice open defecation (OR= 1.72; CI= 1.125-2.615). All the schools did not meet the school sanitation standard of 1 toilet to 30 boys/girls set by the Federal Government of Nigeria. Sustainable sanitation-interventions and maintenance schemes are required to safeguard the health of the students and the community at large.