Incidences of terrorism and proclivity or penchant towards such acts has necessitated the need to examine if secondary school students are inclined towards terrorism, the gender that is most inclined to terrorist tendencies and whether self-esteem issues contribute to terrorism inclination. This is to assist in initiating general and gender specific educational campaign among secondary school students aimed at curbing terrorism in Nigeria. This study aimed to identify the specific gender which is more predisposed to terrorism and to manifesting self-esteem issues among secondary school students. In order to investigate gender differences in terrorism inclination and self-esteem issues among secondary school students in Lagos, 590 students from 8 secondary schools in Lagos State were administered the 10 item Terrorism Inclination Scale by Agbo and Ezeuduji (2010) and the Rosenberg’s self-esteem scale. The participants consisted of 249 males and 341 females aged 9 to 23 years (M = 14.44, SD = 1.58) in Junior and Senior Secondary Schools. The result of a multivariate analysis of variance (MANOVA) used to analyse gender differences in terrorism inclination and self-esteem issues among secondary school students in Nigeria showed a significant influence of gender in terrorism inclination among secondary school students, F (2, 587) = 4.876, p<= 0.01; Wilks’ Lambda = 0.984, partial η2 =0.02 but there was no gender difference in self-esteem level of secondary school students. Male secondary school students reported both higher terrorism inclination (X̅ = 24.56, SD = 8.11) and higher level of self-esteem (X̅ = 21.05, SD = 3.36) than female secondary school students. This study has clearly shown the existence of terrorism proclivity among secondary school students irrespective of their self-esteem level. The need for educators to focus on secondary school students in order to dissuade them from sympathising with terrorists so as to curb the spate of terrorism in Nigeria was discussed.