Yes, but it is much stronger and used in fewer situations. e.g. If you are speaking English to someone you can say, "I'm sorry but I don't understand." You can't say 'I can't fathom'. Also 'fathom' needs an object. 'Understand' dies not. I don't understand - correct. But: I can't fathom his reasons for doing that. I can't fathom why she's so annoyed.

“Fathom” cannot be used in the literal sense as in “I don’t understand that word”. It can refer to an idea or a thought. Also, it is only used in negative sentences

I think both phrases have equal intensity really. “Fathom” is just a little more colloquial I suppose