Disclaimer: I don't own Naruto.
The first time Naruto knows is when Team Seven have their first real training session together. Sakura spares no effort trying to get Sasuke's attention and spends nearly as much time discussing/arguing tactics and maneuvers with Kakashi-sensei. She barely notices Naruto's there.
Later, Naruto goes back to his apartment, props his head on his shoulders as he lies down on the bed and stares up at the ceiling, thinking.
It's then that he realizes that he will never be the most important man in Sakura's life.
The second time comes after Naruto has failed to bring Sasuke home. Naruto comes back barely alive, bandaged head to toe, knowing he will never be the same.
Sakura, despite her weak smiles and denials, is disappointed in him; Naruto knows it. But he knows something else too.
What Naruto knows but refuses to admit to himself, and what Sakura doesn't know at all, is that Sasuke won't be coming home. He won't be coming back. Only someone who had been at the Valley of the End and listened to Sasuke talk could possibly understand.
And Naruto realizes in that moment that Sakura doesn't realize how much that fight has changed him.
There's a barrier between the two of them that is erected in that moment, and is never truly taken down.
The third time is when Naruto sees Sakura for the first time in two years.
They are going through the bell test again, and without warning Sakura opens up a chasm in the earth that reverberates for fully ten seconds and shakes buildings half a mile away. Tsunade couldn't have done better.
As Naruto falls flat on his back and stares in shock at the small, delicate Amazon in front of him, smiling cattily and taunting their sensei with a sickly sweet voice, he has a revelation, one that impresses, shocks, and hurts him.
He doesn't really know Sakura at all.
The second to last time comes in the snowbound Land of Iron.
Naruto's ribs are still aching from the Raikage's attack and his mind is still spinning from the thought that Sasuke is in the Akatsuki when Sakura and company show up. Red flags start going up when he takes a good look at Sakura's face, because her cheeks are unusually pale and her eyes are both red-rimmed and unnaturally bright.
Then, to his immense shock, Sakura tells him that she's in love with him, and pulls him into her embrace.
He pushes her away, disgusted.
Naruto doesn't believe her any more than anyone else watching. Because he can see the lie in her eyes when she says it.
And Naruto knows that if Sakura ever tells him that she loves him again, there will always be a voice in the back of his mind telling him she's lying.
The final time comes when Naruto saves Sakura from Sasuke. She is gasping for breath, rubbing her bruised throat. Naruto surveys the scene, seeing a grim Kakashi and a red-haired girl crumpled on the ground, covered in blood.
As Naruto asks Sakura if she's alright, he sees the hurt in her eyes, along with the pain and all the tormented longing, and knows.
Naruto knows that even if she's willing to kill him, Sakura is still in love with Uchiha Sasuke, and always will be.