The technology relates to articulated autonomous vehicles that can potentially jackknife. To avoid or mitigate such hazardous conditions, the current state of the vehicle is evaluated against the vehicle's planned trajectory, for instance as it drives along a freeway or surface streets. When the evaluation indicates a likelihood of jackknifing, an automated braking approach is implemented using elective braking to stabilize the vehicle. The braking approach can depend on whether the situation involves tractor jackknifing or trailer jackknifing, and one or more different braking mechanisms can be employed for a selective modulation of the braking profile to address actual jackknifing or to prevent the vehicle from entering a jackknifing situation.