The memo does say that Combatant Commanders, who oversee USA troops around the world, could authorize the use of the devices, but only after conducting "a threat-based comprehensive Operations Security survey".
The announcement comes after news stories surfaced earlier this year that fitness apps such as Polar Flow and Strava have been inadvertently giving away locations and habits of US service members on installations around the world.
The order says the applications on personal or government-issued devices present a "significant risk" to military personnel, so those capabilities must be turned off in certain operational areas.
The new restrictions come after the fitness app Strava introduced a "heatmap" feature late past year showing where users workout, inadvertently making it easy to find hidden American military bases overseas.
Defense personnel who aren't in sensitive areas will be able to use Global Positioning System applications if their commanders conclude it doesn't pose a risk.
"It goes back to making sure that we're not giving the enemy an unfair advantage and we're not showcasing the exact locations of our troops worldwide", said Army Col. Rob Manning, a Pentagon spokesman.
The decision follows the discovery of a second fitness smartphone app, called Polar Flow, that allows users to share information about their running routes and related to their location - which can compromise safety and missions if users are located on military bases, intelligence agencies or other sensitive locations.
A portion of the Strava Labs heat map from Kandahar Airfield in Afghanistan, made by tracking activities.
The Pentagon immediately launched a review, noting that the electronic signals could potentially disclose the location of troops who are in secret or classified locations or on small forward operating bases in hostile areas.
In other words, commanders may decide to restrict the use of geolocation capabilities on devices on areas of installations where "sensitive activities" are conducted, Harris said.
While active duty soldiers carry their personal devices to operational areas, they can't take them on missions, so they're left communicating through encrypted radios that haven't changed much since World War II.
Military officials are set to create risk management guidelines and new training for those devices within 30 days, the report said.