Following the merge of #5754 the notebook backend has been integrated with the Jypyter notebook extensions. This requires explicitly enabling the Jupyter notebook extension.

jupyter nbextension enable --py matplotlib

Unfortunatly this is not really documented anywhere yet. Unless you really need something on the master branch I would recommend using the 2.x branch at this stage which is significantly more stable.

There are several other issues with the new notebook backend following that merge see #6414

Since it was really hard to find it for me, here is explained how to get it back running, it's in the package ipympl: https://github.com/matplotlib/jupyter-matplotlib .

Also to install you can't use jupyter nbextension enable --py matplotlib (or at least I could not) but of course then you have to use jupyter nbextension enable --py ipympl.

I'm now getting the same error again, after installing ipympl as @shoeffner said.

@beojan with the latest version of jupyter, notebook, and matplotlib, installing and enabling an extension shouldn't be required. In other words, on my system:

conda create --name=mpltest python=3.6 matplotlib notebook

Is all I need to use %matplotlib notebook in a jupyter notebook.

ipympl and the notebook backend are different backends (both run in the notebook, but they use different js and communication methods).

@beojan it's been a while since you opened the issue - is this still a problem with newer versions of Matplotlib for you?

Closing as there's been no response in a year.