Various design codes and design proposals have been proposed for glued laminated timber beams with round holes, assuming that the entire beam is composed of homogeneous-grade timber. However, in Japan, glued laminated timber composed of homogeneous-grade timber is rarely used for beams. In this study, the difference in the load-bearing capacity of glued laminated beams composed of homogeneous-grade timber and heterogeneous-grade timber with round holes when fractured by cracking was investigated experimentally and analytically. The materials used in the tests were glued laminated beams composed of homogeneous-grade Scots pine timber with a strength grade of E105-F345 and heterogeneous-grade Scots pine timber with a strength grade of E105-F300. Experiments confirmed that although the glued laminated beams composed of heterogeneous-grade timber have a lower material strength in the lamina with holes, its resistance to fracturing due to cracks associated with the holes is almost the same as that of the glued laminated beams composed of homogeneous-grade timber. The stresses acting on the holes in the laminated timber with holes of less than half the beam height were lower in the glued laminated beams composed of heterogeneous-grade timber than in the glued laminated beams composed of homogeneous-grade timber. The ratio of the stresses was found to be approximately equal to the ratio of the maximum bending stress or the maximum shear stress acting on the inner layer lamina, as determined by Bernoulli–Euler theory.