A study was conducted to investigate factors that affect students' poor performance in physical science examinations at Malawi School Certificate of Education and Junior Certificate of Education levels in Community day secondary schools (CDSS) in Lilongwe Rural West Education District in Malawi. Students' performance was collected from schools' Malawi National Examination Board results. Focus group discussion and personal interviews with students, teachers and parents were conducted. Regression analysis, Pearson Correlation and wilcoxon tests were run to determine relationship, correlation and level of significance between the identified factors and students' performance. Analysis of variance, level of significance and standard error deviations (SED) were worked out using SPSS 17.5 version. Results indicate that students' performance in un-approved CDSSs were significantly poor and different from approved CDSS (p<0.01, a = 0.001), day secondary schools (p<0.05, a = 0.05) and national secondary schools in Lilongwe. Students' performance in CDSS without subject specialist was significantly low and different from CDSS with subject specialist (p<0.001, a = 0.05). Students' higher frequency of outings and absenteeism strongly correlated with poor students' performance and greatest record of students' absenteeism in physical science lessons was recorded in rural CDSS and un-approved urban CDSS. Empirical models of the students' performance was more skewed towards poor performers than excellent performers in CDSS, unapproved CDSS, rural CDSS, CDSS without subject specialist, CDSS with majority of students operating from own home or in self-boarding hostels and CDSS with majority of students lacking home support or parental involvement in their education. Lack of or poor home support, high frequency of students' absenteeism, late reporting for classes and absence of subject specialist ranked high in impeding students' performance in both rural CDSS and unapproved CDSS in the study area. Education authorities should consider addressing the raised factors in order to level ground for students' performance in national examinations in all secondary schools.