The study investigated the challenged encountered by school administrators amidst the Covid-19 pandemic and suggested measures for mitigating its impact in secondary schools in Nigeria. Two research questions were posed to guide the study and two hypotheses were tested at 0.05 level of significance. The descriptive survey design was adopted for the study. The entire population of 258 principals was studied without sampling as the size was manageable. A researcher-developed questionnaire 4-point rating scale containing 23 items in two clusters which was validated by three experts from the Faculty of Education, Nnamdi Azikiwe University was used to collect data for the study. Reliability of the instrument was determined through pilot test and data collected were analyzed using Cronbach alpha which yielded reliability coefficients of 0.85 and 0.77 for the two clusters respectively with an overall co-efficient value of 0.81. Mean was used to answer the research questions and standard deviation used to determine the closeness or homogeneity of the respondents’ ratings while t-test was used in testing the null hypotheses at 0.05 level of significance. Findings of the study revealed that failure to maintain social distancing, lack of capacity building of staff, desperation and anxiety on the part of parents and community members, failure to maintain good sanitation practices like regular hand washing among students, and vague orders from school inspectors among others were some of the challenges faced by secondary school administrators during the Covid-19 pandemic. Findings also showed that in order to mitigate the impact of Covid-19 school administrators need to participate in capacity building programmes on Covid-19, project hygiene and health practices in their schools as well as adopt blended learning and technology in teaching students. The location of principals did not influence their opinions. Based on these findings the researchers recommended among others that school administrators should ensure that they attend in-service programmes that will educate them properly on Covid-19 and measures that would help forestall its impact in their schools.