The two small eels were found in a routine fish survey on the River Tud, a tributary of the Wensum in Norfolk.
Increased numbers have also been seen at the New Mills fish pass in Norwich, which was installed eight years ago.
The Environment Agency, which monitors numbers, said it was encouraging but did not "herald the recovery of the species as a whole".
Jez Wood, a specialist at the Environment Agency, said the discovery of the eels on the River Tud was important.
"Two doesn't sound like many, but these are the only small eels we've found on this stretch for years," he said.
"While this does not herald the recovery of the species as a whole, it does show the positive benefit of eel passes at barriers to migration."
The status of the European eel is regarded as "critical", and globally the population has fallen over the past 40 years, with numbers down by as much as 95%, the Environment Agency said.
Barriers to upstream migration is thought to be one of the reasons for the decline.
These reduce access to the freshwater habitat preferred by eels while they mature.
In Norfolk, the Environment Agency is creating passes at several key obstruction areas on rivers to help increase numbers.
It said numbers in Norfolk rivers rose to a record of 34,000 in 2009 after a pass was introduced at New Mills Yard, in Norwich.
Eels have been found in a stretch of river where they have not been seen for nearly 40 years.