Although negation is known to challenge large language models (LLMs), benchmarks for evaluating negation understanding, especially in Korean, are scarce. We conduct a corpus-based analysis of Korean negation and show that LLM performance degrades under negation. We then introduce Thunder-KoNUBench, a sentence-level benchmark that reflects the empirical distribution of Korean negation phenomena. Evaluating 47 LLMs, we analyze the effects of model size and instruction tuning, and show that fine-tuning on Thunder-KoNUBench improves negation understanding and broader contextual comprehension in Korean.