The Rams take a 1-0 lead to Craven Cottage on Monday night after Cameron Jerome's header gave Derby the opening goal in the tie at Pride Park.
Rowett told Sky Sports News, however, that his side must improve ahead of next week's trip to West London.
"It's half time, we spoke about it in the dressing room," the manager said. "I said whilst I was very pleased with our defensive concentration, and with our counter-attacking, we can do it better. We can step out a little bit better at times. It's going to be a tough game down there, because they do what they do well, tire you our mentally and physically.
"We've got to do things at a better level, but we've given ourselves a fantastic opportunity. I was very happy with lots of things. When we showed the quality on the ball we got in some really good positions, I thought we were a counter-attacking threat all night, which is something that we worked on a lot - even though we were at home, we thought we could take advantage of that.
"We know Fulham are a good side and it's that conundrum of trying to press them too high and I thought defensively, we were very, very disciplined. We didn't allow them very many chances, I thought Curtis Davies marshalled [Aleksandar] Mitrovic fantastically well. And actually, I felt we could have picked them off for a second and I'm a little disappointed we didn't."
Derby are seeking promotion to the Premier League for the first time since 2007.