Uncertainty, which is ubiquitous in decision-making, can be fractionated into known probabilities (risk) and unknown probabilities (ambiguity). Although research has illustrated that individuals more often avoid decisions associated with ambiguity compared to risk, it remains unclear why ambiguity is perceived as more aversive. Here we examine the role of arousal in shaping the representation of value and subsequent choice under risky and ambiguous decisions. To investigate the relationship between arousal and decisions of uncertainty, we measure skin conductance response—a quantifiable measure reflecting sympathetic nervous system arousal—during choices to gamble under risk and ambiguity. To quantify the discrete influences of risk and ambiguity sensitivity and the subjective value of each option under consideration, we model fluctuating uncertainty, as well as the amount of money that can be gained by taking the gamble. Results reveal that although arousal tracks the subjective value of a lottery regardless of uncertainty type, arousal differentially contributes to the computation of value—that is, choice—depending on whether the uncertainty is risky or ambiguous: Enhanced arousal adaptively decreases risk-taking only when the lottery is highly risky but increases risk-taking when the probability of winning is ambiguous (even after controlling for subjective value). Together, this suggests that the role of arousal during decisions of uncertainty is modulatory and highly dependent on the context in which the decision is framed.