This study investigated the effects of systematic desensitization and token economy on separation anxiety of Juniour Secondary School Students in Zaria Metropolis. The population of the study consisted of two hundred and eighty seven students with separation anxiety as identified using Spence Children Anxiety Scale. Twenty students from JS II, that are between 13-15 years were selected to participate in the study. The students sampled out for the study were students with high level of separation anxiety. The study employed quasi experimental pretest-posttest design, in which selected students were grouped into two experimental groups. One of the experimental groups was treated with systematic desensitization, and the other with token economy technique. All the participants were exposed to pretest and a posttest. Statistical Package for the Social Science (SPSS) was used, where descriptive statistics of mean and standard deviation was used in answering research questions; hypotheses were tested using paired sample t-test, and analysis of co variance to compare the two variables. The research hypotheses formulated, were tested at 0.05 level of significance. The findings revealed that significant effect exist in the use of systematic desensitization on separation anxiety among Juniour Secondary School Students of Zaria Metropolis (t=4.486 p=.000). The findings also revealed that, token economy has significant effect on separation anxiety among Juniour Secondary School Students in Zaria Metropolis, (t=6.40 p=-.000). There is no significant differential effect of systematic desensitization and token economy technique on post test scores of students with separation anxiety (p=.000). The study also discovered no significant differential effect in the use of systematic desensitization and token economy technique on male and female students with separation anxiety (p=0.52), and (p=0.20). It was recommended that psychologists and counselors should be encouraged by school authorities to use these techniques of systematic desensitization and token economy in handling separation anxiety problems among secondary school students in Zaria Metropolis, Nigeria.