The purpose of the study is to design and implement an enrolment system through web based application intended for higher education institution in Zamboanga Peninsula amidst covid-19 pandemic. The functionalities of the system are guided using Use Cases identified during requirement phase. The existing system encountered several constraints on the process of the enrolment, especially in detecting conflict of course schedules and the availability of slots of the courses offered, handling large number of data, and in cases where modifications or errors in the program that need to be fixed. The methodology used was prototyping to take advantage of the limited experience of users in using computerized systems. It was implemented using Hypertext Pre-processor (PHP) programming language and MYSQL database along with JavaScript, Cascading Style Sheets (CSS), JQuery and Macromedia Dreamweaver as integrated development environment (IDE). The functionalities of the system get the approval of the school administrators allowing the program to be use in an actual enrolment setting.