The paper presents an analysis of the hygrothermal performance of an inverted flat roof with a CLT (cross-laminated timber) structure in a building that meets the requirements of Passive House Standard (PHS) with regards to the potential risk of moisture. The calculations were made in the WUFI®Plus and WUFI®Bio software. The following variants were taken into account: three structure configurations, three different external climates and different scenarios of microclimate control and air change rate. The results of the calculations show that, especially in cooler climates, there is an actual moisture risk in the structure despite the excellent thermal insulation. The structure of the inverted flat roof, due to the use of a tight membrane on the outer side, allows for the partition to discharge the excess moisture only to the inside of the building. Ensuring the comfort of users may require periodic humidification of internal air, which translates directly into an increase in moisture content of the structure. The performed analysis clearly showed that there are no universal solutions. It is important to point out that for the proper performance of inverted wooden roofs, it is crucial to analyse moisture, not only thermal and energy parameters.