A six hectare site was purchased on the corner of Joondalup Drive and Kennedya Drive, and in February 1990, Lake Joondalup Baptist College opened as a secondary school 74 Year 8 students. At a cost of $1.26 million, this was an incredible step of faith for a small church with limited financial resources. The foundation staff consisted of a Principal, an office worker and five teachers. Facilities included three classrooms, a hall and student amenities.
In 1996, Ms Barbara Wadley took up the position of Principal of the College with 530 students from Year 8 to 12 secondary school and 35 staff. During that year, construction commenced on the Lake Joondalup Baptist Primary School, which opened in1997 with 200 students and 11 teachers. The inaugural Principal of the Primary School, Mrs S Smith, was joined by ten teaching staff and an office administrator. The Primary school had an initial enrolment of 240 students. Also during 1997, three new classrooms, an office/storage facility for the Physical Education Department plus a third computer room were completed.