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.

Reprinting the anti-Semitic book was banned after WW2 by Bavaria's regional government, which held the copyright.
The copyright has now expired and Munich's Institute of Contemporary History is to publish a new edition.
New versions are expected in many countries. Historians say the book helps academics understand what happened in the Nazi era.
Its annotated version, with thousands of academic notes, will aim to show that Mein Kampf (My Struggle) is incoherent and badly written, rather than powerful or seductive.
Many Jewish groups have welcomed this particular publication, saying it is important to have access to a critical edition to help explain the Holocaust, reports the BBC's Damien McGuinness in Berlin.
Mein Kampf was originally printed in 1925 - eight years before Hitler came to power.
After Nazi Germany was defeated in 1945, the Allied forces handed the copyright to the book to the state of Bavaria.
The local authorities have refused to allow the book to be reprinted to prevent incitement of hatred, although the book was so widely printed during the war that it remained relatively easily available.
Under European copyright law, the rights of an author of a literary or artistic work runs for the life of the author and for 70 years after his death - in Hitler's case on 30 April 1945, when he shot himself in his bunker in Berlin.
Those rights cease on the first day of January 70 years after the author's death, and so publishers now have free access to the original text.
However, German officials have said they will limit public access to the text amid fears that this could stir neo-Nazi sentiment.
Eels have been found in a stretch of river where they have not been seen for nearly 40 years.
[NEXT_CONCEPT]
For the first time in 70 years, Adolf Hitler's Nazi manifesto Mein Kampf is to be available to buy in Germany.