After Peyton started babysitting for Jake's baby daughter Jenny, they formed a close bond until Jake had to leave with her. But they soon return to Tree Hill and start living with Peyton. The pair helped with the care of Jenny until they confessed their romantic feelings for each other. Eventually Jake had to go to jail and there they confessed their love for each other. But Nicki (Jenny's mother) kidnapped Jenny forcing Jake to leave in search of her, leaving Peyton heartbroken. Peyton later traveled to find Jake afterwards and they had one last weekend together. Peyton proposed to Jake, but they soon both realized that Peyton still had feelings for Lucas as well as Jake and she needed to resolve them. A saddened Peyton returns to Tree Hill, ending their relationship. Jake tells her that if things don't work out between her and Lucas, she knows where to find him, but Peyton leaving is the end of Jeyton.
Peyton begins spending more time with with Jake Jagielski. The pair immediately click and become good friends. Peyton grows close to his baby daughter, Jenny, and Jake trusts her enough to ask her to babysit him, something he's never done before outside of his family. Later at a party, Peyton and Nicki, Jake's ex and Jenny's mother, get into a fight. The season ends with Peyton spending more time with Jake and helping him escape from Nicki, who tries to take their daughter from Jake's grasp.
Hope comes for a depressed, unsure Peyton just as she is about to fall off her mantle and buy some cocaine. Jake comes back to Tree Hill. Lucas Scott was the one who called Jake, knowing that Jake would have a positive effect on her. This proves to be true, sparking a turnaround for Peyton, and she and Jake start a relationship and fall in love. But this happiness is short-lived as Nicki comes back wanting custody of Jenny. Nicki eventually takes Jenny away from Jake and runs off, causing Jake follow her, leaving Peyton alone and heartbroken.
Peyton's father tells her to follow her heart and listen to it, so Peyton decides to give Jake a visit in Savannah; she knows that she still loves him and feels that this will be enough for them to be happy. She renews her relationship with Jake and Jenny, and even goes far enough to propose marriage to Jake, who gladly accepts. But that happiness fades once Jake overhears Peyton say, "I love you, Lucas," in her sleep. Peyton is then forced to confront Jake about the kiss she and Lucas shared on the day of the Tree Hill High shooting. Jake figures that while Peyton loves him, she is in love with Lucas. He tells her to go back to Tree Hill, and to find out if Lucas is still in her heart. If he is not, Jake promises to still be there, waiting. Peyton does as Jake has advised.
- Jake and Peyton's 'catchphrase' is "Someday" in reference to Bryan Greenberg's song. ("Everyday Is a Sunday Evening")
- Jake is the second boy Peyton has slept with and Peyton is the second girl Jake has slept with.
- Jake would often call Peyton "Sharon". Sharon was Jake's first crush who had blonde and curly hair.
- Jake and Peyton would often discuss their future children.
- Peyton would say she wants a son and Jake would want a daughter like Peyton.
- Jake's ex girlfriend Nicki was one of the main causes of strife in their relationship.