diff --git a/src/debugger_requests.jl b/src/debugger_requests.jl
index f271162..4444433 100644
--- a/src/debugger_requests.jl
+++ b/src/debugger_requests.jl
@@ -1,6 +1,17 @@
 # Request handlers
 
 function initialize_request(debug_session::DebugSession, params::InitializeRequestArguments)
+    # The REPL-hosted debugger runs many sessions in one process (VSCodeServer's
+    # `start_debug_backend`), and JuliaInterpreter's breakpoint registry is process-global.
+    # The client only sends `setBreakpoints` for files that still have breakpoints, so a file
+    # whose breakpoints were all deleted between sessions is never mentioned again and its
+    # stale breakpoints would keep firing. Start every session from a clean slate; the client
+    # re-sends the full, current set during the configuration phase that follows.
+    # (Function breakpoints get the same treatment in `DebugEngines.set_function_breakpoints!`.)
+    for bp in copy(JuliaInterpreter.breakpoints())
+        bp isa JuliaInterpreter.BreakpointFileLocation && JuliaInterpreter.remove(bp)
+    end
+
     return Capabilities(
         true, # supportsConfigurationDoneRequest::Union{Missing,Bool}
         true, # supportsFunctionBreakpoints::Union{Missing,Bool}
@@ -167,12 +178,16 @@ function set_break_points_request(debug_session::DebugSession, params::SetBreakp
     @debug "setbreakpoints_request"
 
     filename = params.source.path
+    # `JuliaInterpreter.breakpoint` normalizes the path it is handed and stores that, so the
+    # removal below has to compare against the normalized form or it silently matches nothing
+    # and leaves the old breakpoints in place.
+    normalized_filename = normpath(filename)
 
     # JuliaInterpreter.remove mutates the vector returned by
     # breakpoints(), so we make a copy to not mess up iteration
     for bp in copy(JuliaInterpreter.breakpoints())
         if bp isa JuliaInterpreter.BreakpointFileLocation
-            if bp.path == filename
+            if bp.path == normalized_filename
                 @debug "Removing breakpoint at $(bp.path):$(bp.line)"
                 JuliaInterpreter.remove(bp)
             end
diff --git a/test/test_debugsession.jl b/test/test_debugsession.jl
index 4fed2c9..9bedf87 100644
--- a/test/test_debugsession.jl
+++ b/test/test_debugsession.jl
@@ -111,3 +111,49 @@ end
     @test DefaultTerminationTarget.ran == true
     @test count(==("terminated"), events) == 1
 end
+
+@testitem "initialize clears file breakpoints left over from an earlier session" begin
+    import JuliaInterpreter
+
+    # The REPL-hosted debugger serves many sessions from one process, and the client only
+    # sends `setBreakpoints` for files that still have breakpoints. A file whose breakpoints
+    # were all deleted between sessions is therefore never mentioned again, so unless the
+    # adapter clears the process-global registry itself the deleted breakpoints keep firing
+    # for the rest of the REPL's life (julialang.org discourse #138981).
+    JuliaInterpreter.remove()
+
+    target = joinpath(@__DIR__, "stale_breakpoint_target.jl")
+    JuliaInterpreter.breakpoint(target, 2)
+    @test any(bp -> bp isa JuliaInterpreter.BreakpointFileLocation, JuliaInterpreter.breakpoints())
+
+    # A new session's first request, with no `setBreakpoints` following it.
+    session = DebugAdapter.DebugSession(IOBuffer())
+    DebugAdapter.initialize_request(session, DebugAdapter.InitializeRequestArguments(adapterID="julia"))
+
+    @test !any(bp -> bp isa JuliaInterpreter.BreakpointFileLocation, JuliaInterpreter.breakpoints())
+end
+
+@testitem "setBreakpoints removes previous breakpoints for a non-normalized source path" begin
+    import JuliaInterpreter
+
+    # `JuliaInterpreter.breakpoint` stores the normalized path, so the removal pass has to
+    # compare against the normalized form of `source.path` or it matches nothing and leaves
+    # the old breakpoints behind.
+    JuliaInterpreter.remove()
+
+    target = joinpath(@__DIR__, "sub", "..", "breakpoint_target.jl")
+    source = DebugAdapter.Source(path=target)
+
+    DebugAdapter.set_break_points_request(
+        DebugAdapter.DebugSession(IOBuffer()),
+        DebugAdapter.SetBreakpointsArguments(source=source, breakpoints=[DebugAdapter.SourceBreakpoint(line=2)])
+    )
+    @test count(bp -> bp isa JuliaInterpreter.BreakpointFileLocation, JuliaInterpreter.breakpoints()) == 1
+
+    # The client now reports that the file has no breakpoints left.
+    DebugAdapter.set_break_points_request(
+        DebugAdapter.DebugSession(IOBuffer()),
+        DebugAdapter.SetBreakpointsArguments(source=source, breakpoints=DebugAdapter.SourceBreakpoint[])
+    )
+    @test count(bp -> bp isa JuliaInterpreter.BreakpointFileLocation, JuliaInterpreter.breakpoints()) == 0
+end