diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
index 013705e34b..96034968ef 100644
--- a/src/systems/abstractsystem.jl
+++ b/src/systems/abstractsystem.jl
@@ -1888,6 +1888,15 @@ function linearization_function(sys::AbstractSystem, inputs,
         generate_initializesystem(
             sys, guesses = guesses(sys), algebraic_only = true),
         fully_determined = false)
+    # HACK: some unknowns may not be involved in any initialization equations, and are
+    # thus removed from the system during `structural_simplify`.
+    # This causes `getu(initsys, unknowns(sys))` to fail, so we add them back as parameters
+    # for now.
+    missing_unknowns = setdiff(unknowns(sys), unknowns(initsys))
+    new_parameters = [parameters(initsys); missing_unknowns]
+    @set! initsys.ps = new_parameters
+    initsys = complete(initsys)
+
     if p isa SciMLBase.NullParameters
         p = Dict()
     else
diff --git a/test/downstream/linearize.jl b/test/downstream/linearize.jl
index 38df060332..6e9a4a070d 100644
--- a/test/downstream/linearize.jl
+++ b/test/downstream/linearize.jl
@@ -195,3 +195,66 @@ lsys, ssys = linearize(sat, [u], [y]; op = Dict(u => 2))
 @test isempty(lsys.B)
 @test isempty(lsys.C)
 @test lsys.D[] == 0
+
+# Test case when unknowns in system do not have equations in initialization system
+using ModelingToolkit, OrdinaryDiffEq, LinearAlgebra
+using ModelingToolkitStandardLibrary.Mechanical.Rotational
+using ModelingToolkitStandardLibrary.Blocks: Add, Sine, PID, SecondOrder, Step, RealOutput
+using ModelingToolkit: connect
+
+# Parameters
+m1 = 1
+m2 = 1
+k = 1000 # Spring stiffness
+c = 10   # Damping coefficient
+@named inertia1 = Inertia(; J = m1)
+@named inertia2 = Inertia(; J = m2)
+@named spring = Spring(; c = k)
+@named damper = Damper(; d = c)
+@named torque = Torque()
+
+function SystemModel(u = nothing; name = :model)
+    eqs = [connect(torque.flange, inertia1.flange_a)
+           connect(inertia1.flange_b, spring.flange_a, damper.flange_a)
+           connect(inertia2.flange_a, spring.flange_b, damper.flange_b)]
+    if u !== nothing
+        push!(eqs, connect(torque.tau, u.output))
+        return ODESystem(eqs, t;
+            systems = [
+                torque,
+                inertia1,
+                inertia2,
+                spring,
+                damper,
+                u
+            ],
+            name)
+    end
+    ODESystem(eqs, t; systems = [torque, inertia1, inertia2, spring, damper], name)
+end
+
+@named r = Step(start_time = 0)
+model = SystemModel()
+@named pid = PID(k = 100, Ti = 0.5, Td = 1)
+@named filt = SecondOrder(d = 0.9, w = 10)
+@named sensor = AngleSensor()
+@named er = Add(k2 = -1)
+
+connections = [connect(r.output, :r, filt.input)
+               connect(filt.output, er.input1)
+               connect(pid.ctr_output, :u, model.torque.tau)
+               connect(model.inertia2.flange_b, sensor.flange)
+               connect(sensor.phi, :y, er.input2)
+               connect(er.output, :e, pid.err_input)]
+
+closed_loop = ODESystem(connections, t, systems = [model, pid, filt, sensor, r, er],
+    name = :closed_loop, defaults = [
+        model.inertia1.phi => 0.0,
+        model.inertia2.phi => 0.0,
+        model.inertia1.w => 0.0,
+        model.inertia2.w => 0.0,
+        filt.x => 0.0,
+        filt.xd => 0.0
+    ])
+
+@test_nowarn linearize(closed_loop, :r, :y)