The Secondary section of New Day Secondary School has been divided into five levels:
Class VI 11.5 to 12.4 years old
Class VII 12.5 to 13.4 years old
Class VIII 13.5 to 14.4 years old
Class XI 14.5 to 15.4 years old
Class X
The curriculum followed by the classes 6 to 8 is Oxford textbook while class 9 and 10 follow the Sindh Board. The school follows the Matriculation system of examination for class 9 and 10. They appear for SSC examinations annually and have been producing 100% result ever since. The curriculum delivery methodology in the secondary school classrooms encourages a student-centered approach. With skills such critical thinking, teamwork, drawing connections between the studied text and the outside world, students are well equipped to perform efficiently.
Since the students of class 6, 7 and 8 are no longer children, they go through the junior youth empowerment program. This program guides and channelizes their growing potentials towards the path of service to their community. This program is facilitated by an animator, who is an older friend to them. While those students of class 9 those who are interested get trained to serve as animators or teachers of children classes. They continue serving in class 10 as well.