The rights group said Lebanese civilians can end up in military courts for any interaction with security services or their employees.
The courts are under the defence ministry's jurisdiction and conduct closed sessions, and their judges are often military officers who are not required to have any legal training.
"It has become abundantly clear that civilians cannot get a fair trial in Lebanon's military courts," said Lama Fakih, deputy Middle East director at HRW.
"Military courts have no business trying civilians, and Lebanon should end this troubling practice."
The group said hundreds of civilians were tried before military courts in 2016, but a precise figure was not available.
The Union for Protection of Juveniles in Lebanon said the figure included 355 children.
HRW said it had received reports that defendants were being tortured during military interrogations and forced confessions, including from children, were being used as evidence.
And it said the courts "have used their broad jurisdiction to intimidate or retaliate against individuals for political reasons and to stamp out dissent".
Among those facing trial before military courts are activists arrested in 2015 for protesting government inaction over a waste collection crisis.
Fourteen protesters face up to three years in prison during a trial scheduled for later this month.
HRW urged Lebanon to open military courts up to public observers, and noted that international law prohibits the use of military courts for civilians when ordinary courts are still functioning.
"The least Lebanon can do is ensure that its citizens aren't being sentenced in secret by a specialised court behind closed doors," Fakih said.
