The sides also meet on Sunday in the league ahead of a two-legged European encounter next month with the winner advancing to the quarter-finals.
Valencia have enjoyed a resurgence of late to lift the pressure on coach Gary Neville but Negredo was still downbeat at the prospect of facing Athletic.
"Athletic are not the team we wanted right now - it would have been better for us to meet later," he told He told Uefa's official website.
"Now we are on a good run of form and I hope we manage to get through, although we know we're up against difficult opponents.
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"It's going to be a very tight tie. They are also on a good run. Now we have to play two games against them and we'll see what happens."
Athletic boss Ernesto Valverde also admitted it was going to be tough for his side to progress but relished what he described as a "great tie".
He said: "It's a tough draw, we keep getting tough draws - in the Copa del Rey and the Europa League.
"We're playing them on Sunday too. It's going to be an open tie, we know Valencia are currently in one of their best moments of the season. They have won four in a row and have great players. It's a great tie."