The young teacher had difficulty

[Bassim]

I am wondering if my sentence sounds natural.

The young teacher had difficulty in maintaining discipline in her class. When one half calmed down, another played up.

 

[jutfrank]

When one half calmed down, the other (half) played up.

As soon as would also work well instead of When.

 

[GoesStation]

I'd write acted up​ rather than "played up".

 

[teechar]

Consider taking our the first "in". Also, I would use "one lot" instead of "one half". If you do use "one half" in a sentence, use "the other half" subsequently instead of "another half". There are only two halves.
I would also change "played up" to "started acting up."

[Edit: I'm getting sluggish in my middle (old?) age. Beaten to it by jutfrank and GoesStation.]

 

[Bassim]

I will repeat my sentence as an exercise.

The young teacher had difficulty maintaining discipline in her class. As soon as one lot calmed down, the other started acting up.