The 38-year-old reality TV star is reportedly concerned for Scott, who has been spotted partying with various different women over recent weeks.
A source said: "Kourtney is worried for Scott, as are Scott's friends and the whole Kardashian family. They are really worried for him.
"They aren't angry – just concerned – because he's clearly going through something."
Scott, 34, has recently been romantically linked to the likes of Bella Throne, Chantel Jeffries and Maggie Petrova.
But the Kardashian family feel Scott's recent behaviour is a function of his own unhappiness, which has reportedly been triggered by Kourtney dating model Younes Bendjima.
Another source told Us Weekly: "The partying and photos emerging are symptomatic of situations they've had in the past with him where he has been in a really bad place, mentally."
Earlier this month, meanwhile, Scott admitted to being a "horrible sex addict".
The TV star revealed he's addicted to love-making during a candid conversation with Kris Jenner, Khloe Kardashian, Kim Kardashian West and his ex.
Speaking on 'Keeping Up with the Kardashians', Scott confessed: "I'm a sex addict. I'm a f***ed up, horrible sex addict."
Scott acknowledged his problem after he angered the Kardashians by bringing another woman with him on a family vacation in Costa Rica earlier this year.
Kourtney confronted Scott about the decision, calling his behaviour "disrespectful".
She said: "On a family vacation, don't you think it's inappropriate and disrespectful?
"To me, to your kids and to all my family? There's a level of respect and appropriateness that should just be known, but apparently, it's not."
Kourtney also rubbished Scott's explanation, accusing him of "playing the victim".