- At one point, Lara has to remove a parasitic worm from Jonah's arm. They contemplate giving him a name, and Jonah recommends Eli. Eli is a cousin of Jonah's who was always trying to get under his skin.
- During a flashback of young Lara climbing around Croft Manor and putting her neck on the line, she narrates the situation to herself, play-acting an adventurer. Except for a brief and blinding moment of self-awareness when she's on the roof;"Why do I do these stupid things?"
- After going through a temple and uncovering a cryptic mural, Lara begins speculating what it means. She voices her thoughts in saying that she needs to find a cave or temple entrance shaped like a jaguar's mouth, expecting to search far and wide. Turns out, Abby's already found it. Lara's borderline dumbstruck at how easy it was.
- It doesn't take long for Lara to notice Abby's obvious interest in Jonah. She tries to hide her amusement long enough for Abby to tell them about the ruins behind the village, 'til Lara can no longer maintain her composure and finally has to excuse herself. Jonah doesn't get why she's leaving.
- Two kids can be found in Kuwaq Yaku playing around with a frog they had caught. One boy insists it would be funny to shove a firework up the poor frog's butt - much to the disgust of his friend.
- One of the relics you can find is a plastic penguin lawn ornament decorated in Paititian style paint and headdress. Lara has to keep herself from laughing when she narrates the description.
- The ending of the DLC mission: The Pillar, has this. After traversing through dangerously high and windy obstacles and a fight with the local Trinity members, Lara and Q'orianka finds out that the shield they were searching for would bring more chaos instead of help and agrees to burn it. As they toss the shield into a nearby fire, Jonah passes by and his face can be summed up as: WTF?Jonah: Is that the shield?(Lara and Q'orianka stares back at him)Jonah: I don't even want to know why you're burning that. I'm just glad you made it back. Again.
- A sidequest set in Mission of San Juan has a (sorta) hidden funny moment if you switch on the 'immersive' dialogue mode (in which the natives will speak the local language instead of English). One bit of this quest will lead Lara to seeing an old lady who is rumoured to be a witch. If you set the immersive mode off, the lady can be heard laughing rather dismissively at this particular rumour, however if you switch the immersive mode ON, she lets out a genuinely wicked cackle that lends credence to this rumour. Her laughter was so witchy that even Lara is taken aback.
- Llama Croft can be found as a "pose" in Photography mode. It's a Llama that takes the place of Lara. The game gives no reason for including this in the game, as the presence of Llamas in the game are as background animals in and around Paititi, and seems to have been added by the development team because of the pun.
- At one point, Lara and Unuratu are trying to enter a chamber, Lara is wearing the Tomb Guard outfit and Unuratu is in her regular dress. As the door opens enough to admit Unuratu, it suddenly slams shut and Lara hears the sounds of a struggle between Unuratu and one of the guards. This goes on for about a minute, with Lara's concern written all over her face. Finally, the noise ceases and the door slides open again. There is Unuratu, saying simply, "C'mon, let's go!"
Funny / Shadow of the Tomb Raider