Police arrested on Monday morning at least ten students of Rumbek National Secondary School and two teachers over protest.
The students raised concerns over lack of lessons.
According to the students, the school head teacher was given a notice three weeks ago that the academic secretary should resign, but did not respond.
The students blame the Academic Affairs Secretary Martin Mabeny who later resigned following the strike.
He earlier promised to bring in more teachers because of acute shortage, but the students were not patient enough.
School head teacher Ustaz Gabriel Malieny Marek, says the strike had nothing to do with lack of teachers.
He instead accused Mawac, Deputy Academic Secretary for inciting the students to protest, which he denies.
Rumbek National Secondary School, one of the leading and historical schools in South Sudan is now closed for three days.