Thyme is a rich source of bioactive phytochemicals and it is frequently used in folk-medicine to treat gastroenteritis irritations. The current study was performed to examine the potential of Thymus vulgaris aqueous extract (TV-AE) to protect against delayed gastric emptying (DGE) and colonic constipation in rats. Stomach ulcer was caused by a single oral dose administration of indomethacin (INDO) (30 mg kg⁻¹ of body weight). Constipation was induced following intravenous intoxication of rats with vinblastine (VINB) (2 mg kg⁻¹ of body weight) for one week. The effect of TV-AE at two graduated doses (100 and 200 mg kg⁻¹) on DGE, gastrointestinal transit (GIT) and constipated rats and biochemical parameters was estimated using phenol red, charcoal meal test and colorimetric methods, respectively. The phytochemical-profile of TV-AE was explored using high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization-mass spectrometry (HPLC-PDA/ESI-MS). INDO and VINB caused a significant reduction in (P < 0.05) DGE and GIT and colonic motility dysfunction. TV-AE consumption remarkably (P < 0.05) attenuated the DGE (from 58.56% to 69.871%) and difficulty in evacuating stools (from 48.5 to 55.5 fecal pellets per rat) and balanced the GIT (65% to 71%). These GI-ameliorative effects were accompanied by reversed INDO/VINB-related oxidative changes, lipid-metabolism alteration and intracellular pathway moderation. HPLC-PDA/ESI-MS-analysis identified several chemical constituents including rosmarinic acid, quinic acid, luteolin-7-o-glucoside, protocatechuic acid and trans-cinnamic acid. Thus, TV-AE bioactive components may be used as medicinal substances to regulate/attenuate gastrointestinal–physiological activities and disturbances, which support its pharmacological use.