While this series is the type to be filled with a mixture of both HeartWarmingMoments and {{TearJerker}}s, this series also has its fair share of NightmareFuel.

* The final episode of season 3 where Natsume [[spoiler: 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 [[spoiler: 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, [[spoiler:the Kimono Youkai]] on Episode 5 of Natsume Yuujinchou San when it jerked and hastily crawled towards Natsume and Tanuma [[spoiler: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''. [[spoiler:It's just a nightmare.]]
** The creep-tastic hovering NightmareFace Youkai that shows Natsume the way to a [[ItMakesSenseInContext tree stump with a bamboo shot sticking out of it]]. In return he wishes to [[ImAHumanitarian feast on his guts]].
** The Shadow sent to kill Natsume due to a death curse, [[NothingIsScarier completely featureless]], [[ParanoiaFuel 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 [[spoiler: 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 [[spoiler: to meet possibly the same end as your friend]].