The company’s net income fell to C$958 million in the third quarter ended Sept. 30, from C$972 million, a year earlier.
On a per share basis, earnings rose to C$1.27 from C$1.25.
Excluding items, the company earned C$1.31 per share, missing the average analysts’ estimate of C$1.32 per share, according to Thomson Reuters I/B/E/S.
The company said operating expenses rose by 10 percent to C$1.76 billion.
CN reported an operating ratio of 54.7 percent, up from 53.3 percent, a year earlier.
The lower the operating ratio, a key industry metric which measures operating costs as a percentage of revenue, the more efficient the railroad.
Total revenue rose 6.9 percent to C$3.22 billion.
Last week, CN rival Canadian Pacific Railway Ltd (CP.TO) reported a better-than-expected quarterly profit on higher shipments of crude oil, coal and potash.
Reporting by Taenaz Shakir in Bengaluru; Editing by Shounak Dasgupta