In October 1998, the Breisgau S-Bahn operated a special train with a Regio-Shuttle.
Feasibility studies in the spring of 2004 showed that the line would have a favourable cost-benefit ratio.

After a three-week trial operation, the opening ceremony was held for the resumption of passenger services on 27 August 2006.
From 2006 to 2012, it was operated on certain Sundays and public holidays as a special event service.
In 2006, these operated on a total of 14 days.
Daily services consisted of six trips in each direction on a two-hour frequency, only stopping at Neuenburg.
The operator for the German section was DB Regio AG Südbaden on behalf of Nahverkehrsgesellschaft Baden-Württemberg (Local transport company of Baden-Württemberg, NVBW) and for the French section was SNCF on behalf of the Région Alsace.
These were operated with diesel multiple units of French class X 73900 (called Baleine Bleue in French and Blauwal in German, meaning "blue whale") with 82 seats.
On German territory the French trains are operated on behalf of Deutsche Bahn.

The resumption of a scheduled passenger traffic on the line in the long term was sought.
It has therefore been partly modernised since 2009 and, among other things, the mechanical interlockings have been replaced by electronic interlockings.
Since December 2009, six pairs of trains have run every two hours from Neuenburg mostly continuing to Offenburg.

The track has also been studied as an option for a rail link to EuroAirport Basel Mulhouse Freiburg.
The railway companies of France, Germany and Switzerland proposed, in a memorandum prepared in 2003 and called Trinationale platform Basiliensis, that goods originating in France and Switzerland and continuing on the German Rhine Valley Railway use the Müllheim-Mulhouse route as the preferred future option for bypassing the bottleneck in Basel.
This would require the construction of a new south curve at Müllheim.

There have been demands from the Upper Rhine region for an extension of the LGV Rhin-Rhône TGV line, which was commissioned in 2011, to Freiburg.
As part of the preliminary studies for the 2003 Federal Transport Infrastructure Plan (Bundesverkehrswegeplan), an upgrade of the section on the German side of the Rhine to two tracks and permitting speeds of up to 160 km/h was estimated to cost €40 million.
It was decided not to include the project in the Plan.

Since 9 December 2012, there are up to seven services daily between Müllheim and Mulhouse, with at least one pair of trains running directly to and from Freiburg Hauptbahnhof.
Since then, a French X 73900 (called Baleine Bleue in French and Blauwal in German, meaning "blue whale") has been used, which also stops in Bantzenheim.

Since the end of August 2013, a pair of TGVs run between Freiburg and Paris on the line.

After the completion of the third and fourth tracks as part of the Karlsruhe–Basel high speed line, an hourly service from Mulhouse via Müllheim and Freiburg to Sasbach is envisaged under the Breisgau S-Bahn 2020 proposal.
In October 1998, the Breisgau S-Bahn operated a special train with a Regio-Shuttle. Feasibility studies in the spring of 2004 showed that the line would have a favourable cost-benefit ratio.
After a three-week trial operation, the opening ceremony was held for the resumption of passenger services on 27 August 2006. From 2006 to 2012, it was operated on certain Sundays and public holidays as a special event service. In 2006, these operated on a total of 14 days. Daily services consisted of six trips in each direction on a two-hour frequency, only stopping at Neuenburg. The operator for the German section was DB Regio AG Südbaden on behalf of Nahverkehrsgesellschaft Baden-Württemberg (Local transport company of Baden-Württemberg, NVBW) and for the French section was SNCF on behalf of the Région Alsace. These were operated with diesel multiple units of French class X 73900 (called Baleine Bleue in French and Blauwal in German, meaning "blue whale") with 82 seats. On German territory the French trains are operated on behalf of Deutsche Bahn.
The resumption of a scheduled passenger traffic on the line in the long term was sought. It has therefore been partly modernised since 2009 and, among other things, the mechanical interlockings have been replaced by electronic interlockings. Since December 2009, six pairs of trains have run every two hours from Neuenburg mostly continuing to Offenburg.
The track has also been studied as an option for a rail link to EuroAirport Basel Mulhouse Freiburg. The railway companies of France, Germany and Switzerland proposed, in a memorandum prepared in 2003 and called Trinationale platform Basiliensis, that goods originating in France and Switzerland and continuing on the German Rhine Valley Railway use the Müllheim-Mulhouse route as the preferred future option for bypassing the bottleneck in Basel. This would require the construction of a new south curve at Müllheim.
There have been demands from the Upper Rhine region for an extension of the LGV Rhin-Rhône TGV line, which was commissioned in 2011, to Freiburg. As part of the preliminary studies for the 2003 Federal Transport Infrastructure Plan (Bundesverkehrswegeplan), an upgrade of the section on the German side of the Rhine to two tracks and permitting speeds of up to 160 km/h was estimated to cost €40 million. It was decided not to include the project in the Plan.
Since 9 December 2012, there are up to seven services daily between Müllheim and Mulhouse, with at least one pair of trains running directly to and from Freiburg Hauptbahnhof. Since then, a French X 73900 (called Baleine Bleue in French and Blauwal in German, meaning "blue whale") has been used, which also stops in Bantzenheim.
Since the end of August 2013, a pair of TGVs run between Freiburg and Paris on the line.
After the completion of the third and fourth tracks as part of the Karlsruhe–Basel high speed line, an hourly service from Mulhouse via Müllheim and Freiburg to Sasbach is envisaged under the Breisgau S-Bahn 2020 proposal.
Müllheim–Mulhouse railway