"Get out, JOH," shouted the students, who threw rocks and burned tires to block the road in front of the National Autonomous University of Honduras, in the eastern part of Tegucigalpa.
Many of the protesters had their faces concealed behind masks or scarves.
The tear gas fired by anti-riot police forced the students to retreat onto the campus, while they threw stones.
No injuries were immediately reported.
The demonstrations in violence-wracked Honduras came one day after opposition leftists took to the streets, answering a protest call by ex-president Manuel Zelaya to urge the conservative Hernandez to step down.
Sunday's protests brought thousands into the streets across the country. Police also used tear gas in some instances to clear the protest areas.
Hernandez began his second term on January 27, 2018 after being re-elected in a November 2017 vote decried as fraudulent by the Zelaya-led opposition alliance.
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