Background: Stroke patients usually have arm weakness, which affects trunks and arms. Objective: To investigate the effects of paretic side and non-paretic side arm training on trunk control and upper limb functions. Design: Randomized Controlled Trial (single blind). Methods: Twenty patients with stroke in hospital were enrolled in the study. Twenty subjects were randomly assigned to paretic side arm training group (PATG, n = 10) or non-paretic side arm training group (NATG, n = 10). Trunk impairment scale (TIS) was used for trunk control, and box and block test (BBT) was used for upper limb function. Training was conducted for 4 weeks. Results: PATG showed significant difference in TIS (static balance, dynamic balance, coordination, total score) and BBT. NATG showed significant differences in static balance, and dynamic balance and total score except for coordination and BBT. PATG also showed a more significant difference in BBT and coordination and total score than NATG. Conclusions: The arm training performed on the paretic side are more effective than those performed on the non-paretic side in improving both upper limb function and trunk control in stroke patients.