[3] As with all motor nuclei of cranial nerves, it is located near the midline (i.e. in the medial midbrain).

It is situated immediately below the nucleus of the oculomotor nerve (CN III) (the only other cranial nerve with a nucleus in the midbrain besides the mesencephalic nucleus of trigeminal nerve, which functions in preserving dentition).

The trochlear nucleus is unique in that its axons run dorsally and cross the midline at the trochlear decussation (located in the superior medullary velum) in the midbrain before emerging from the brainstem posteriorly/dorsally.

[citation needed] In other words, trochlear nucleus on one side gives rise to the trochlear nerve on the contralateral side.

A lesion of the trochlear nucleus thus affects the contralateral eye, whereas lesions of all other cranial nuclei affect the ipsilateral side.