Svein Arne Hansen said the 800m runner, who has served a two-year drugs ban, is welcome at the European Championships, which start in Amsterdam on Wednesday.
"With her brave statements and brave actions, she's really going out there to protect our sport," said Hansen.
Stepanova, 30, has also been cleared to run as a neutral at the Rio Olympics.
Stepanova was banned for two years in 2013 for doping offences but her revelations, along with those of husband Vitaly - a former drug-testing official - helped expose the doping problem in her country.
"Everyone in Russia is saying it makes no sense that Yuliya is eligible to compete," Vitaly said.
"But we never accused athletes, it was the system we accused."
The Russian athletics federation has been banned from international competition since November, after a World Anti-Doping Agency report - commissioned following claims made in a German TV documentary  - found evidence of state-sponsored doping.
The documentary's claims of widespread wrongdoing stemmed principally from allegations made by Stepanova and her husband.
"She's very welcome because she's done a great job for the sport," Hansen added.
However, France's Renelle Lamote, this year's leading European woman over 800m, has not welcomed Stepanova's return to competition.
"I am against the fact that athletes who once doped can come back," she said.
"Whether they denounced the system or not, it's an injustice."
Vitaly does not think Stepanova, who has not competed since September 2015, is likely to produce a top performance in the Netherlands.
"She never stopped training. But she had not done the necessary training to run two minutes because she did not know she would be allowed to compete," he said.
"She also has had some minor injuries lately so she is not in great shape yet.
"I don't know what she will do but it is not about winning now, it's just about trying to compete, respecting the competition and not putting the result ahead of the rules.
"She is just happy to be able to compete again and whatever she can run, she will run."
Russian doping whistleblower Yuliya Stepanova has been described as a "symbol" for clean competitors by the president of European Athletics.