A group of three poachers shot dead the rhino in wee hours near Hahsora forest camp before taking away the horn, the official said.
Hearing gunshots, the Forest Vigilance Squad searched the area and found the carcass of the pachyderm, he said.
A massive dragnet has been spread with the help of police to trap the poachers, the official added.
Another adult rhino was killed and its horn taken away earlier this year at the sanctuary.
The sanctuary had reopened for tourists on November 2 after a routine closure of four months during the monsoons.
Pobitora has leopards, wild boar, barking deer, wild buffalo, etc, and is also home to more than 2000 migratory birds and various reptiles, the official said.
