The International Committee of the Red Cross (ICRC) said it would initially man two entry and exit points three days a week in the northern districts of Vavuniya and Mannar.
The ICRC had pulled out of the two locations last week after both security forces and Tamil Tiger rebels stepped up shelling in the areas, putting the lives of its staff and civilians at risk.
"In discussions with the Sri Lankan government and the Liberation Tigers of Tamil Eelam (LTTE) over the recent incidents, the ICRC obtained the security guarantees it needed to resume its task," said ICRC spokesman Davide Vignati.
Government troops and Tamil rebels have been locked in combat following the breakdown of a 2002 Norwegian-arranged truce. Over 5,000 people have been killed in the last 18 months.
In the latest violence in the frontier town of Vavuniya, the defence ministry said a soldier died when an army sentry point was shelled by suspected Tamil Tigers late Tuesday.
There was no immediate comment from the Tamil