Andres Iniesta put Thierry Henry through on the left and the Frenchman worked clear for a shot. Schalke goalkeeper Manuel Neuer fumbled the ball at the near post, Henry put it back across the face of the goal and the 17-year-old Krkic tapped it in at the far post in the 12th minute."I am very pleased with the result. The team worked well and deserves compliments," Barcelona coach Frank Rijkaard said. "We got into the game well and the early goal helped, but we then we had more problems in the second half."
"We played well on the flanks, we won the ball, we controlled most of the game. Bojan made all the right decisions on the field and behaved like an experienced player."
Two-time winner Barcelona remained unbeaten in the Champions League this season and remained on course for its second title in three years, although a 3-2 loss to Real Betis on Saturday dropped it to third in the Spanish championship.
"I didn't think the team would have so much respect," Schalke coach Mirko Slomka said. "We only applied pressure in the second half and made some threats."
"We should have put them under more pressure from the start. It's not going to be easy in Barcelona but we wouldn't be going there if we didn't have any hope," Slomka said.
Schalke was playing its first Champions League quarterfinal and at times looked overmatched by the Catalan side, even though the Spanish were without the competition's top scorer Lionel Messi, Ronaldinho and Deco.
The match, before a capacity crowd of 53,951, was played under a closed roof because of heavy rain.
Iniesta should have put the visitors ahead even before the goal, when Xavi had put him through, but Neuer blocked the ball with his foot.
With Xavi and Iniesta controlling the midfield, Barcelona controlled the tempo and limited Schalke to several attempts from distance.
Halil Altintop's attempt was deflected early in the second half, with Barcelona goalkeeper Victor Valdes on the wrong foot, but the ball went wide and Schalke made no use of the resulting corner.
Valdes then dropped a shot by Christian Pander but Barcelona's defenders cleared the ball.
Barcelona's defense allowed Heiko Westermann to close on goal unchallenged in the 58th, but the defender's shot went high.
Iniesta replied for Barcelona but Neuer covered the shot.
Neuer was forced off his line to clear a long ball from Gianluca Zambrotta with Krkic charging.
Schalke's best chance came when Pander found Fabian Ernst at the edge of the area but his shot was deflected and trickled outside the post.
With Barcelona's defense beginning to give away space, Altintop narrowly missed the target.
Westermann connected with a free kick from Pander but headed high in the 81st.
In injury time, Rafinha delivered a cross from the right and Schalke's central defender Marcelo Borden rose above the defenders, but his header went over the crossbar.
"We had too much respect for them," Schalke midfielder Gerald Asamoah said. "The coach told us at halftime to put them under more pressure and we tried to do that. We played better but we could not score."