His injury was not described as life-threatening.
The man was caught on the horn of a bull named ‘Ilustrado’, some 50 seconds into the run as the bulls reached the Plaza del Ayuntamiento, in front of the City Hall.
The horn ripped through his left thigh but the injury was described by the hospital as “not serious”.
Five other men were injured during the run, which was made more dangerous by slippery cobblestones after a morning rainshower, and were being treated at the Navarra Hospital in Pamplona.
Wednesday's run featured bulls from the Núñez del Cuvillo ranch and lasted just 2 minutes 32 seconds. The festival comes to a close on Thursday.
Eleven others have been gored in earlier runs and dozens have been treated for cuts, bruises and strains suffered during falls or crushes during the morning runs.
The daily runs see people dashing with six bulls along a winding, 850-metre (more than half a mile) course through narrow streets to the city's bull ring, where the animals are killed by professional matadors in an afternoon bullfight.
This year's San Fermin festival has been marred by a spate of sex attacks. Police have recieved 15 separate complaints of assault so far this year, including six for “sexual aggression” which under Spain's penal code includes rape.
A total of 15 men have been arrested including five accused of gang raping a woman and recording the violation on a mobile phone.