If you go by the meaning of their nominal cognates, there is a substantial difference: the adjective "cranial" derives from Latin "cranium" (skull) while the adjective "cerebral" is a derivate of the Latin "cerebrum" (brain).
But I am aware that this isn't your question. - What contexts are you thinking of?
I can think of at least one not-so-medical context where both of these adjectives are not interchangeable: a paleontologist speaks of "cranial fossils", he wouldn't speak of "cerebral fossils". But that's obvious.
Urban Dictionary provides definitions for colloquial uses of these adjectives and gives this interesting example sentence:
"He wanted to be cerebral but came across very cranial" (Art. "cranial")
According to the dictionary, a cranial person is stupid, while a cerebral person is an attentive and intelligent person.
But is this alleged colloquialism common anywhere or is it just an urban myth?
As @Ashwin states, in a medical context "cranial" refers to the skull, whereas "cerebral" refers to the brain. In other words they describe different bits of the body, and therefore are not interchangeable.
In more colloquial usage, "cerebral" tends to mean the brain as a source of thoughts (in other words, "the mind"), rather than the squishy physical organ. However, "cranial" still generally refers to the skull or the head.
So again, not interchangeable.