Although some findings have reported the medicinal properties of Jimson weed (Datura stramonium L.), there exist some serious neurological effects such as hallucination, loss of memory and anxiety, which has been reported in folklore. Consequently, the modulatory effect of alkaloid extracts from leaf and fruit of Jimson weed on critical enzymes of the purinergic [ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase), ecto-5′-nucleotidase (E-NTDase), alkaline phosphatase (ALP) and Na+/K+ ATPase] system of neurotransmission was the focus of this study. Alkaloid extracts were prepared by solvent extraction method and their interaction with the activities of these enzymes were assessed (in vitro) in rat brain tissue homogenate and in vivo in rats administered 100 and 200 mg/kg body weight (p.o) of the extracts for thirty days, while administration of single dose (1 mg/kg body weight; i.p.) of scopolamine served as the positive control. The extracts were also investigated for their Fe2+ and Cu2+ chelating abilities and GC–MS characterization of the extracts was also carried out. The results revealed that the extracts inhibited activates of E-NTPDase, E-NTDase and ALP in a concentration dependent manner, while stimulating the activity of Na+/K+ ATPase (in vitro). Both extracts also exhibited Fe2+ and Cu2+ chelating abilities. Considering the EC50 values, the fruit extract had significantly higher (P < 0.05) modulatory effect on the enzymes' activity as well as metal chelating abilities, compared to the leaf extract; however, there was no significant difference (P > 0.05) in both extracts' inhibitory effects on E-NTDase. The in vivo study revealed reduction in the activities of ENTPDase, E-NTDase, and Na+/K+ ATPase in the extract-administered rat groups compared to the control group, while an elevation in ALP activity was observed in the extract-administered rat groups compared to the control group. GC–MS characterization revealed the presence of atropine, scopolamine, amphetamine, 3-methyoxyamphetamine, 3-ethoxyamhetamine cathine, spermine, phenlyephirine and 3-piperidinemethanol, among others in the extracts. Hence, alterations of activities of critical enzymes of purinergic signaling (in vitro and in vivo) by alkaloid extracts from leaf and fruit of Jimson weed suggest one of the mechanisms behind its neurological effects as reported in folklore.