Emotional difficulties are associated with both authorized and unauthorized school absence, but there has been little longitudinal research and the temporal nature of these associations remains unclear. This study presents three-wave random-intercepts panel models of longitudinal reciprocal relationships between teacher-reported emotional difficulties and authorized and unauthorized school absence in 2,542 English children aged 6 to 9 years old at baseline, who were followed-up annually. Minor differences in the stability effects were observed between genders but only for the authorized absence model. Across all time points, children with greater emotional difficulties had more absences, and vice versa (authorized: ρ = .23–.29, p < .01; unauthorized: ρ = .28, p < .01). At the within-person level, concurrent associations showed that emotional difficulties were associated with greater authorized (β = .15–.17, p < .01) absence at Time 3 only, but with less unauthorized (β = −.08–.13, p < .05) absence at Times 1 and 2. In cross-lagged pathways, neither authorized nor unauthorized absence predicted later emotional difficulties, and emotional difficulties did not predict later authorized absence at any time point. However, greater emotional difficulties were associated with fewer unauthorized absences across time (β = −13–.22, p < .001). The implications of these findings are discussed.