The Scottish Emergency Rider Volunteer Service (ScotsERVS) say the theft of the equipment, which contains all their funding information, is "catastrophic."
The metallic red Toshiba Satellite was stolen from the charity's office, based in Glasgow's Southern General Hospital, after thieves broke into the campus.
Police are investigating the incident and are urging people with information to come forward.
Volunteers of ScotsERVS, which was launched in Glasgow in 2011 by Jason Kelly and his partner Sarah Cameron, give their spare time to assist the NHS in delivering urgent supplies, including donor breast milk, blood, plasma, samples, vaccines and medical files to hospitals.
They travel by motorbike or car to get the supplies to the hospital as quickly as possible.
The charity was rolled out to the whole of Scotland in June but is based at NHS Greater Glasgow and Clyde (NHSGGC).
Ms Cameron, 29, said the laptop was usually kept in a locked up location but had been borrowed by another member of the group and used in the office.
She said: "The laptop has all our funding information on it.
"It has the history of our funding applications, it has prepared packages for grants we're applying for. It has everything on it that helps us to survive.
"It is catastrophic for it to be missing."
Ms Cameron said the theft could "affect the lives of sick kids and others who benefit from our service".
A spokesman from Strathclyde Police said: "We are appealing for any information about the identity of those responsible for the theft of the laptop and its recovery due to the significance of the data stored on it and the implications for future funding for the charity."
A spokeswoman from NHSGGC added: "We can confirm that office space on the Southern General Campus which we gift to the charity ScotsERVS was broken into on September 5.
"It is very disappointing when any thefts occur on hospital grounds.
"The hospital is monitored by CCTV and all footage has been provided to Police Scotland as part of their inquiries into the theft."