A low‐carbohydrate and high‐protein (LC‐HP) diet demonstrates favorable impacts on metabolic parameters, albeit it leads to a decline in hippocampal function with the decreased expression of hippocampal insulin‐like growth factor‐1 receptor (IGF‐1R) among healthy mice. However, the precise mechanisms underlying this phenomenon remain unexplored. Eight‐week‐old male C57BL/6 mice were divided into the LC‐HP diet‐fed group (25.1% carbohydrate, 57.2% protein, and 17.7% fat as percentages of calories; n = 10) and the control diet‐fed group (58.9% carbohydrate, 24.0% protein, and 17.1% fat; n = 10). After 4 weeks, all mice underwent the Y‐maze test, followed by analyses of hippocampal mRNA and miRNA expressions. We revealed that feeding the LC‐HP diet suppressed working memory function and hippocampal Igf1r mRNA levels in mice. Sequencing of hippocampal miRNA demonstrated 17 upregulated and 27 downregulated miRNAs in the LC‐HP diet‐fed mice. Notably, we found decreased hippocampal mRNA levels of low‐density lipoprotein receptor‐related protein 6 (Lrp6), a gene modulated by miR‐539‐3p, in mice fed the LC‐HP diet. Furthermore, a significant positive correlation was observed between Lrp6 and Igf1r mRNA levels in the hippocampus. These findings suggest that LC‐HP diets may suppress hippocampal function via the miR‐539‐3p/Lrp6/Igf1r axis.