The vascular bundle system in the panicle neck of rice (Oryza sativa L.) connects the culm to the panicle and transports assimilates. The number of vascular bundles in the panicle neck (VBN) is correlated with the diameter of the panicle neck (DPN), but there are few reported QTLs for DPN. We conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross between ‘Asominori’ and ‘IR24’ and detected three QTLs—qDPN5, qDPN6, and qDPN11—on chromosomes 5, 6, and 11. The qDPN5, qDPN6, and qDPN11 were in the same position as the QTLs for VBN reported in previous studies. Within the RILs, there was a significant positive correlation between DPN and VBN. In segregating populations, each QTL had a distinct effect on both values. Analysis of chromosome segment substitution lines showed that qDPN5 and qDPN11 affected DPN and qDPN6 affected VBN. Through substitution mapping, we narrowed down the region of qDPN5 and qVBN5.2 to 960 kbp between KNJ8 Indel385 and RM18926, and the region of qVBN6 to 750 kbp between C5 Indel5756 and KNJ8 Indel493. Due to the weak effect of qDPN6 in the ‘IR24’ genetic background, the location of qDPN6 could not be determined.