Rail operators, which moved record-high Canadian oil volumes at the beginning of the year, witnessed a plunge in crude volumes as energy companies cut production in the face of falling demand due to coronavirus-driven lockdowns.
The company's operating ratio, a closely watched measure of operating expenses as a percentage of revenue, rose to 59.9% from 57.9%.
However, grain and fertilizers carloads, the amount of freight loaded into cars during a specified period, rose 12% in the quarter as reduced shipment of crude and consumer goods has freed up railway space, boosting movement of grains.
Smaller rival Canadian Pacific Railway Ltd earlier in the day missed Wall Street estimates as shipments declined during the pandemic.
On an adjusted basis, Canadian National earned C$1.38 per share, missing analysts' average estimates of C$1.46, according to IBES data from Refinitiv.
Net income fell to C$985 million ($750.36 million), or C$1.38 per share, in the quarter ended Sept. 30 from C$1.20 billion, or C$1.66 per share, a year earlier.
Revenue fell 11% to C$3.41 billion.
($1 = 1.3127 Canadian dollars)
(Reporting by Shreyasee Raj in Bengaluru; Editing by Devika Syamnath)