There’s a tiny bit of overlap between the two. Runabouts can be assigned to large starships as auxiliary craft, the same way shuttlecraft are. And shuttlecraft can have the amenities (though on a reduced scale) of a runabout.

Star Trek Deep Space Nine Runabout

But generally, runabouts are designed to operate independently of a starship. To that end, runabouts almost always have a full complement of basic equipment, such as food replication and waste recycling, two-person transporter, and a warp drive. They sometimes have the capability of being fitted with high-end sensor packages, or weapons packages or having the living quarters replaced with a cargo module, but they aren’t multi-purpose multi-competency ships.

Power; The runabouts have a warp core, which is significantly more compact and automated than any previous design. This endowed the Star Trek Deep Space Nine Runabout Development Logo runabout with greater endurance, range, and speed (up to Warp 5) than conventional shuttlecraft, which were powered by capacitors (charged by the mothership). The warp core also provided power for mission-specific equipment, such as science labs, sensors, and weapons.
Accommodation; A shuttlecraft was essentially a flying box, sometimes with a partition separating the cargo/passenger area from the pilot(s). A runabout had a distinct flight deck, for up to four crew, with a transporter pod. Beyond the midsection was a compact habitat module. This included basic sleeping quarters and ablutions and catering facilities.

Star Trek Deep Space Nine Runabout Development Logo

Modularity; The midsection of a runabout was a detachable module that could be changed according to the runabout’s current mission. Modules were available for cargo, passengers, sensors, weapons, science labs, and medical facilities. Also, a rollbar could be installed over the habitat module to support a pod containing mission specifics equipment.

Shuttles are smaller, can usually only carry about 8 people, pilot and co-pilot included. They also weren’t intended for long-duration travel, even in the 24th Century when shuttles had warp drive. They were usually meant to transport personnel and supplies within interplanetary distances. Either because the Star Trek Deep Space Nine Runabout Development Logo transporters weren’t working, or because materials being shipped were too volatile to risk using the transporter.

Runabouts, or as I like to call them ‘Shuttles on Steroids’ were basically mini-starships. They were larger, and modular meaning they could be modified to perform anything from Long-Range Scout to a troop transport, as opposed to shuttles which were purpose-built. They could also have enough fuel for traveling interstellar distances, making them great if you wanted to travel from one starbase to another, but didn’t want to use a Starship to do so. Because of this, they replaced Shuttles on Starbases, and larger Starships (like the Akira and Galaxy classes) began carrying them.

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