As timber tends to be weak against the load perpendicular to grains, it can be important to study the consequences of applying loads perpendicular to larch cross-laminated timber (CLT) composed of multiple larch laminae. Compression tests were conducted perpendicular to the in-plane and out-of-plane grains of Japanese larch CLT. Out-of-plane average compressive strength, average yield strength, and average compressive stiffness perpendicular to the grain of the larch CLT were 11.94 N/mm2, 7.30 N/mm2, and 7.30 N/mm3, respectively, whereas the in-plane average compressive strength, average yield strength, and average compressive stiffness perpendicular to the grain of the larch CLT were 21.48 N/mm2, 21.18 N/mm2, and 18.72 N/mm3, respectively. The in-plane compressive strength and yield strength showed a statistically significant relationship with the density of CLT, the modulus of elasticity measured by longitudinal vibration (MOELV), and the average MOELV of the laminae constructing the cross-laminated timber. The in-plane yield strength was affected by the MOELV of the outer laminae and the average MOELV of the larch cross-laminated timber. The compressive strength properties were most affected by the loading surface of the CLT. The variation between the moisture content and compressive strength properties of the CLT, however, was not statistically significant.