It happened at the Heath Pharmacy Ltd on Free School Lane in Halifax earlier this afternoon (Friday).
On the business' Facebook page a spokesperson said: "You may have heard that we were robbed at knife point this afternoon. We are all ok and unharmed but quite shaken up."
They apologised for the disruption to daily business as the incident had left them unable to hand out prescriptions.
The statement added: "Thank you to everyone who agreed to come back at a later time for your prescriptions as we were in no fit state to deal with them."
West Yorkshire Police were last night unable to comment on the alleged incident.