While this series is the type to be filled with a mixture of both Heartwarming Moments and Tear Jerkers, this series also has its fair share of Nightmare Fuel.
- The final episode of season 3 where Natsume almost disappeared and became a youkai's pet, with the threat of his family being eaten. It's mask with the eyes and creepy plastered smile didn't make it any less creepier (and when Sensei scared it off, it's mask shattered in half, it still had that smile). And just think what happened if the Fujiwaras DIDN'T come meet Natsume at that time.
- Some of those Youkai are as creepy as can possibly be.
- Like that cabinet scene involving Kakura, the Kimono Youkai on Episode 5 of Natsume Yuujinchou San when it jerked and hastily crawled towards Natsume and Tanuma with just its one hand and leg.
- Once Natsume hands suddenly start to excrete sand, two of his fingers simply drop off, then his face shatters into pieces. It's just a nightmare.
- The creep-tastic hovering Nightmare Face Youkai that shows Natsume the way to a tree stump with a bamboo shot sticking out of it. In return he wishes to feast on his guts.
- The Shadow sent to kill Natsume due to a death curse, completely featureless, slowly inching towards his house, eventually making its way inside. After he tries to run away from it he wakes up to discover that not only has it gotten a whole lot quicker, it's mere inches away from his face, jaws open.
- The Omibashira Arc. From the screams to the eaten ayakashi and the blood stained room to the design of Omibashira himself. Just think being an unsuspecting ayakashi who was invited with a friend, promised protection for your gift, temporarily separated with your friend until you realize he/she is gone and look for them only to meet possibly the same end as your friend.
