The online portal Compass Education crashed about 9 am on Wednesday due to heavy traffic from students across Victoria.
But it soon recovered and students were able to start term two.
GSSC executive principal Genevieve Simson said many students would be learning from home, while others were allowed to attend school if their parents were working.
She said some parents also had to wait in line at McGuire and Wanganui campuses to collect borrowed laptops for their children to access Compass.
Ms Simson said it would be a strange experience for the students and teachers.
“We've never done this type of learning before,” she said.
“It will take a bit of time for all of us to get used to it. We're also using Teams for teachers to video call their students.
“For those at school, they still need to wear school uniform. We are sticking to the 1.5 m rules and limiting it to 10 students per classroom."
In a statement, Compass Education said: "Our team of Melbourne-based developers are continuing to boost the platform capabilities to meet the demands of these unpredictable and uncertain times.”
Borrowed laptops will still be available for collection until the end of the week.
Students who need to attend school because their parents are working, must apply with the school first.
For more information visit gssc.vic.edu.au/
Read more about Greater Shepparton Secondary College
One-hundred GSSC students to receive free laptops and internet in Australian first
Local Year 12s anxious they may need to study into next year for ATAR