The aim was to undertake secondary data analysis from a three-arm randomised feasibility trial of high intensity interval training (HIIT), moderate intensity continuous training (MICT), and usual care control in adults with Crohn's disease (CD; n = 36), with a primary focus on exploring affective and enjoyment responses. Twenty-five participants with quiescent or mildly-active CD were randomised to one of the two exercise groups: HIIT (n = 13) and MICT (n = 12). Both groups were offered thrice weekly sessions for 12 weeks. MICT consisted of cycling for 30 minutes at 35% peak power (Wpeak), whereas HIIT involved ten 1-minute bouts at 90% Wpeak, interspersed with 1-minute bouts at 15% Wpeak. Heart rate (HR), differentiated ratings of perceived exertion for legs (RPE-L) and central (RPE-C), along with feeling state (Feeling Scale; FS) were measured at 92.5% of each session. Enjoyment was measured at the end of training using the Physical Activity Enjoyment Scale (PACES). Post-hoc exploratory analysis involved a mixed-model two-way ANOVA to compare HR, RPE-L, RPE-C and FS for the exercise sessions in weeks 1, 6 and 12 between groups. Overall, HR was greater (p < 0.01) during HIIT (173 ± 8 bpm) compared with MICT (128 ± 6 bpm). Similarly, RPE-L and RPE-C responses were greater overall (p = 0.03 and p = 0.03, respectively) during HIIT (5.5 ± 1.6 and 5.1 ± 1.7, respectively) compared to MICT (3.3 ± 1.5 and 2.9 ± 1.5, respectively). Overall, FS was 2.2 ± 1.9 for HIIT and 2.1 ± 1.4 for MICT with no effect of treatment group (p = 0.25) or time (p = 0.94). There was also no significant difference in PACES scores between HIIT (99.4 ± 12.9) and MICT (101.3 ± 17.4; p = 0.78). The findings suggest HIIT and MICT protocols elicited similar enjoyment and affect in adults with quiescent or mildly-active CD.