diff --git a/lib/ModelingToolkitBase/src/systems/problem_utils.jl b/lib/ModelingToolkitBase/src/systems/problem_utils.jl
index 291e8e2e44..d1073f0452 100644
--- a/lib/ModelingToolkitBase/src/systems/problem_utils.jl
+++ b/lib/ModelingToolkitBase/src/systems/problem_utils.jl
@@ -537,7 +537,13 @@ function evaluate_varmap!(
         ir::IRStructure{SymReal}, varmap::AtomicArrayDictSubstitutionWrapper, vars;
         limit = 100, allow_symbolic = false
     )
-    subber = Symbolics.FixpointSubstituter(SU.IRSubstituter{true}(ir, varmap); maxiters = limit, warn_maxiters = !allow_symbolic)
+    # Use `FPSubFilterer{Nothing}` so substitution descends into operator calls such as
+    # `Initial`, matching the generic `fixpoint_sub` path. The default IR filterer treats
+    # operators as atomic, leaving `Initial`-dependent guesses unresolved.
+    subber = Symbolics.FixpointSubstituter(
+        SU.IRSubstituter{true}(ir, varmap; filterer = Symbolics.FPSubFilterer{Nothing}());
+        maxiters = limit, warn_maxiters = !allow_symbolic
+    )
     for k in vars
         v = get(varmap, k, COMMON_NOTHING)
         v === COMMON_NOTHING && continue
diff --git a/lib/ModelingToolkitBase/test/initializationsystem.jl b/lib/ModelingToolkitBase/test/initializationsystem.jl
index 103f3f58ae..67b3741c5c 100644
--- a/lib/ModelingToolkitBase/test/initializationsystem.jl
+++ b/lib/ModelingToolkitBase/test/initializationsystem.jl
@@ -1610,6 +1610,24 @@ end
     @test integ1[X1] ≈ 1.0
 end
 
+@testset "Initial-dependent array parameter guesses" begin
+    @variables X1(t) X2(t)
+    @parameters k1 k2 Γ[1:1] = missing [guess = [Initial(X1 + X2)]]
+    eqs = [D(X1) ~ k1 * (Γ[1] - X1) - k2 * X1]
+    @named osys = System(
+        eqs, t, [X1], [k1, k2, Γ]; observed = [X2 ~ Γ[1] - X1]
+    )
+    osys = complete(osys)
+    prob = ODEProblem(
+        osys,
+        [X1 => 1.0, X2 => 2.0, k1 => 0.1, k2 => 0.2],
+        (0.0, 1.0)
+    )
+
+    @test prob[X2] == 2.0
+    @test prob.ps[Γ[1]] == 3.0
+end
+
 if @isdefined(ModelingToolkit)
     @testset "Trivial initialization is run on problem construction" begin
         @variables _x(..) y(t)