The Little Runaway (https://www.fanfiction.net/s/4312807/1/) - maxandkiz
Eight year old Sammy runs away after an argument with his dad. Written for the SFTCOLARS Theme Challenge. Warning: strong language and some violence.

Desperately Seeking Sam (http://archiveofourown.org/works/802639) - morgana07
Sam’s gone. Did he walk away? Dean believes so…until things begin adding up in a way that he doesn’t like & finally figures out the real reason his brother didn’t look for him. Follow Dean’s path as he learns some truths, faces some truths, deals with old & new enemies alike all as he fights to find Sam before it’s too late to save him from a fate worse than anything they’ve faced. Angsty/furious/protective!Dean & Hurt/ really hurt/confused/drugged!Sam

The First Cut is the Deepest (http://www.fanfiction.net/s/4777400/1/) - sammygirl1963
TeenChester: When a training accident goes horribly wrong, John blames his youngest for almost killing Dean causing Sammy to run away. Will he survive on his own until his brother finds him? Sam is 14 and Dean has just turned 19. Hurt Boys!

Storm of Emotions (https://www.fanfiction.net/s/4185988/1/) - sammygirl1963
After a fight with his dad, will a run away Sammy survive the coming storm! Hurt/Sick Sam, Angsty Dean, Guilty John!

Learning to Breathe (http://samdean.archive.nu/viewstory.php?sid=2479) - Jassy
When he was fifteen, Sam confessed his romantic feelings to his brother. Rejected and unable to face his brother again, Sam runs away. In an effort to stay off his father's radar, he turns to a life of crime to get by. As it turns out, he's pretty good at it.

Worth Saving Me (http://archiveofourown.org/works/363508) - wolfish_willow
Pre-series AU, Alternating POV. Nearly 9 years after Dean's little brother ran away, Dean walks into the Roadhouse for the first time. He's taken by surprise at the sight of Sam, now an adult, acting like a brother to a blond named Jo, and calling the bar's owner, Ellen, "Mom". Sam looks terrified to see him and the shot gun Ellen trains on Dean's chest leaves him angry and confused when all he wants to do is grab his brother into a hug and never let him out of his sight again. And soon, Dean will find out the truth behind why and how Sam left them 8 years ago.

Runaway (https://www.fanfiction.net/s/4260208/1/) - J.A. Carlton
After getting Dean in trouble at school Sam decides his big brother’s better off without him and runs away. WeeChesters! Angst! Warverse Compliant…

You Always Hurt the One You Love (https://www.fanfiction.net/s/8185107/1/) - Justine Samulet Delarge
9-year-old Sammy is mad he doesn’t get a normal life. John’s anger turns physical. Dean takes the brunt of it, and when he goes to talk to Sam afterward, things go terribly wrong, and Sammy runs away. Pre-series. NO romantic/adult connection. Just brother bond.


That doesn´t exactly fit your general request but is very similar:

Taken (https://www.fanfiction.net/s/6937634/1/) - 427-67Impala (or on AO3 (http://archiveofourown.org/works/200728))
The fact that Sam started the Apocalypse isn't as secret as he thinks. He's on his own, away from Dean, and there are some hunters that aren't keen to forgive. They have Sam, and they want payback - but they don't know Dean is coming for his baby brother.