An alternative precommercial thinning technique results in trees being cut higher up the stem compared to the normal method using a brush saw. The aims of this study were to investigate if primary infection of Heterobasidion spp. on precommercial thinning stumps of Norway spruce and birch is influenced by stump height and to test the control efficacy of stump treatment with Phlebiopsis gigantea on precommercial thinning stumps of Norway spruce. Small Norway spruce and birch trees were felled on five sites in southern Sweden and their stumps subjected to natural spore infection. For each species, two treatments of stump height were created: 15 and 100 cm. Half of the Norway spruce stumps were treated with P. gigantea. After two months, 896 stumps were sampled and infection by Heterobasidion spp. was quantified. The height of stumps did not significantly influence infection frequency or size of infection on either tree species. Untreated Norway spruce stumps had an infection frequency of 55% while 31% of the treated stumps were infected. The control efficacy of stump treatment in terms of reduced relative infected area was 61–65%. The area occupied by Heterobasidion spp. on birch stumps was generally small, on average 0.4 cm2 per infected stump, although 15% of the stumps were infected. The risk of primary infection in Norway spruce dominated stands should be considered when precommercial thinning is conducted but the control efficacy and economy of stump treatment warrants further investigation before practical recommendations can be made.