School-based instructional supervision (SBS), which is conducted by principals,rnvice principles and department heads at the school level, is aimed to helprnteachers to become effective in their teaching and in bringing about improvedrnstudent learning. The purpose of the study was to investigate the perception ofrnteachers towards SBS, the practice and the major factors affecting SBSrnpractices in secondary schools of Afar regional s tate. To realize this purpose,rnhow secondary school teachers practice school based instructional supervision,rnhow teachers perceive the purpose of supervision and what factors affect thernpractice of school-based supervision were raised as bas ic questions. Tornanswer the basic questions both quantitative and qualitative research designrnwere used. The method employed here was descriptive survey method. Thernstudy was conducted in three secondary schools in zone one of Afar RegionalrnState. Thus, the supervisees (teachers), department heads, vice principals,rnprincipals and external supervisor from the Regional Education bureau used asrnsources of data. These respondents were selected by simple random andrnpurposive sampling techniques. Data were collected from these respondentsrnusing questionnaire, interview and focus group d iscussion. Then thernquantitative data that involve frequency counting were coded and processedrnusing SPSS. The qualitative data is analyzed with dp.;::,th examination of relatedrndocument. The finding of the study revealed that teacher's perception towardsrnSBS was negative; school based supervision was not conducted in properrnmanner and teachers have no proper perception about school basedrnsupervision. It was also found out that supervisors lack training to conductrnSBS. Thus, depending on the result of the findings the researcher recommendsrnthat collegial supervis ion, experience s haring and training to be given to schoolrnbased supervisors. It is recommended that school based supervisors mustrncreate awareness about SBS and have to practice it to improve instructionrnrather than using it for performance appraisal.