The trick I published below works much better in later versions.
You can apply a stroke to a clipping group with an ease and control the alignment directly form the Stroke panel. The Divide and Add effects are not required anymore, and holes are treated as expected.

Files

There is a workaround I came up with, that solves this problem, almost completely, except for some minor limitations.
Please study the files attached.

Some notes about the method:

1. Two Graphics Styles are created to apply these quickly.

2. You can't change the alignment when a style is applied, but can change everything else — color, weight, etc. This happens because
Ai doesn’t let us toggle the alignment, when a stroke is applied to a clipping group — even with this method. One part believes clipping groups can’t have aligned strokes (and thus Stroke panel has controls deactivated), but another part knows the stroke is aligned (and Appearance panel says so). That’s why styles were built using simple shapes.

3. Divide effect should not remove empty paths in its options — otherwise the stroke won’t bound the clipping path itself — even when filled, the mask is considered to be empty by the effect.

4. No holes are possible with this method (see clip_stroke_inside-outside_hole) — you will see the background through them, but no stroke.

5. Method won’t work for clipped images, texts, meshes, blends, etc. Only simple graphics.

This is nowhere an ultimate solution, but a mere hack.
Please upvote the request to make it a legal proper functionality.
If I can come up with something like this, engineers at Adobe surely can do it better.

This is still happening.

Having the same issue....

me too, please fix

Some reasons why this is happening. More details below - hope this helps explain the dynamics at play.

There are three ways of creating clipping groups in Ai:

1. Select two overlapping paths, Object > Clipping Mask > Make.
2. Select a path, go to Draw Inside Mode > create/paste anything.
3. Select an image and click 'Mask' button.

Masking path, by design, cannot contain advanced fills, strokes and effects. Inline with this rule, creating clipping groups using first method drops all fills and strokes of the masking path. There is a minor exception in the second method where 'basic' stroke and fill is retained, but effects or advanced/multiple fills get dropped.

In all clip groups, the clipping path gets a little less priority than the clipped object. This can be seen when trying to select the contents of the clip group - the selection hits are only recognized on clipped content, even when a fill is available in the clipping path.

Issue highlighted here mentions that a new stroke is being added over the entire layer and is being moved below the content. Any new stroke in appearance panel, is an effect. And as described in point #2, clipping paths cannot contain effects.

Also worth mentioning here is that the new stroke added at layer level in appearance panel, and then moved below is not a right course for workaround as it pushes the stroke below all fills - notice only half the thickness of stroke is visible (the other half is getting hidden behind the fill).

The expectation mentioned in this report is to enable strokes on clipping groups via appearance panel - for that the limitations mentioned in #2 would have to be go away. A detailed study of technical possibilities, use-case analysis and user research would have to be done on currently existing content, as well as clipping groups that would get created in future.

Me too! I hope they answer this question. I also can't use the strokes in the Appearance tab on a clipping mask...

When I create a clipping mask, I can set stroke color and size for Clipping mask path object and it works well. But I need to set stroke align of my Clipping mask from Center to Inside. Immediately when I change Stroke align to Inside (or Outsize) - it is disappear from object display.

How to reproduce this bug in Adobe Illustrator CC 2018:

1. Create Circle inside Rectangle as clipping mask

2. Select Clipping mask Path object (Rectangle) and apply any stroke to them (eg 1pt black) - it shows normally.

3. Change Stroke align to Inside or Outside - it will disappear!

4. Change back Stroke align to Center - it will return!

Why this happens and where is the source of this problem? Why Clipping mask stroke works only with Center aligned stroke?

How can I force Inside (Outside) stroke for clipping mask stroke? If this is Illustrator bug, maybe some workarounds exists?