Disposal of designated waste that is radioactive contaminated by the Fukushima nuclear accident is a primary issue in Japan. This study examined the determinants of public acceptance of siting a repository for designated waste, focusing on affective reaction, procedural fairness, and trust. The study presumed that affective reaction moderates the effects of procedural fairness and trust on public acceptance. To examine the presumption, the study implemented a hypothetical scenario experiment that manipulated two factors: an opportunity of voice as an antecedent of procedural fairness and similarity value to the authority as a component of trust. 289 people participated in the web-based experiment. Participants were randomly assigned to one of four conditions: procedural fairness (voice vs. no voice) × trust (similarity vs. no similarity) factorial design associated with acceptance of siting investigation for designated waste. The experiment measured affective reaction to the siting, and evaluations of procedural fairness, trust, public acceptance in the decision-making process. Results indicated that affective reaction, procedural fairness, and trust determined public acceptance. Moreover, the interactive effect of affective reaction × trust was found. A process analysis indicated that the effect of trust on public acceptance was strengthened when the affective reaction was negative. However, the interactive effects of affective reaction × procedural fairness and trust × procedural fairness were not found. The study showed that trust was susceptible to affect. This study suggested the significance of trust for people with a strong affective reaction in promoting the public acceptance of siting a facility for designated waste.