Layer chicks are usually transported early in life, experiencing immediate post-hatch food and water deprivation and various transport-related stressors with potentially negative long-term consequences for learning, cognition and welfare. In contrast, as chicks are only temporarily exposed to these stressors, the experienced stress could be sub-chronic which may improve cognitive flexibility. The aim of this exploratory study was therefore to investigate the acute and long-term effects of on-farm hatching (OFH) compared to conventional hatching. Dekalb White layer chicks were subjected to either OFH (n = 47) with ad libitum access to feed and water or temporary post-hatch resource deprivation and eight hour transport (RDT; n = 42). Physical and behavioural measures were collected to examine short-term effects of the treatment procedures. To determine longer term effects, treatment differences in learning and cognitive flexibility were assessed in a Y-maze using several paradigms (reversal, attentional-shift, extinction) between 4 and 12 weeks of age (WOA). Compared to OFH chicks, RDT had: greater corticosterone levels after transport (F1,19 =8.15, p = 0.01, RDT (16.24 ± 1.20 ng/mL) vs. OFH (8.13 ± 1.20 ng/mL) and post-recovery (F1,19 =4.93, p = 0.04; RDT (11.69 ± 1.35 ng/mL) vs. OFH (5.31 ± 1.37)), and lower body mass after resource deprivation and transport (F2258 =9.7, p < 0.001, RDT (33.14 ± 0.33 g) vs. OFH (37.62 ± 0.28 g)). Performance of activity behaviours (foraging, drinking, resting, wing-assisted running) after transport exhibited treatment by time interactions. Additionally, a tendency for OFH being heavier than RDT chicks was observed up to 11 WOA. The majority of birds learned the initial association in the Y-maze between a reward and location (77% of n = 19 RDT and n = 29 OFH chicks) or light stimulus (91% of n = 12 RDT and n = 11 OFH chicks). Subsequently, a number of chicks reached the learning criterion in the location reversal (24% of n = 13 RDT and n = 24 OFH chicks) and the light-to-location attentional-shift (47% of n = 11 RDT and n = 10 OFH chicks), and most of these chicks succeeded in the following extinction paradigm (80% of n = 3 RDT and n = 7 OFH chicks). No treatment effects were detected in any phase of cognitive testing. In conclusion, treatment affected behaviour and health parameters suggesting RDT animals were recovering from resource deprivation and transport. Continued treatment differences in body mass throughout rearing demonstrated long term effects as well although no effects on initial learning and cognitive flexibility were identified. Future work is needed to determine what mechanisms are responsible for the observed health and behavioural differences.