In 1848 he was second wrangler.

There were two prizes, called Dr.Smith's, for the two most distinguished mathematicians of the year.

The senior wrangler's papers had the first of these; for the second, Mackenzie was neck and neck with a Trinity College man, and the question was only decided by the fact that Dr.Smith had desired that his own college (Trinity) should have the preference.
After this he became tutor and fellow of his college, taking private pupils, and at the same time preparing for Holy Orders, not only by study of books, but by work among the poor, with whom his exceeding kindness and intense reality gave him especial influence at all times.
He was ordained on the Trinity Sunday of 1851, and took an assistant curacy at a short distance from Cambridge, his vigorous powers of walking enabling him to give it full attention as well as to his pupils and to the University offices he filled.

His great characteristic seems always to have been the tenderest kindness and consideration; and in the year when he was public examiner, this was especially felt by the young men undergoing an ordeal so terrible to strained and excited intellect and nerves, when a little hastiness or harshness often destroys the hopes of a man's youth.
With this combination of pastoral work and college life Mackenzie was perfectly satisfied and happy, but in another year the turning-point of his life was reached.

A mission at Delhi to the natives was in prospect, and the Rev.J.S.Jackson, who belonged to the same college with him, came to Cambridge in search of a fellow-labourer therein.