Leverkusen looked set for a famous win before a dramatic late twist saw former Leverkusen star Kai Havertz equalise from the penalty spot in the 89th minute.
The German side had taken the lead just after half-time through captain Robert Andrich, but Arsenal escaped with a draw after the referee awarded a spot kick following a challenge on Noni Madueke.
Hjulmand made it clear after the match that he strongly disagreed with the decision.
"I have mixed feelings," the Leverkusen coach said. "It was a very good performance against a top team. Of course we are disappointed with the last scene. A 1-0 would obviously have been much better than a 1-1. I don't see a penalty there, but that's how it is."
Despite his frustration, the Dane praised his players for their disciplined display against one of Europe's strongest sides.
"It was a top performance against a top team. We didn't concede many chances. We were active and played well with the ball," Hjulmand added. "Of course it's frustrating that we only drew 1-1, but we travel to London with hope."
Hjulmand also suggested the pressure now sits firmly on Arsenal ahead of the return leg.
"I believe there is a lot of pressure on Arsenal. We must and we can deliver another strong performance. We want to cause an upset."
Young Leverkusen forward Christian Kofane shared his coach's optimism after an encouraging performance.
"Anything is possible in football - we saw that today," Kofane said. "We played against one of the best teams in the world and had them on the brink of defeat. That must give us hope."
The decisive second leg will take place on Tuesday, 17 March at Emirates Stadium in London, where a place in the Champions League quarter-finals will be at stake.