diff --git a/compiler/noirc_evaluator/src/ssa/opt/simplify_cfg.rs b/compiler/noirc_evaluator/src/ssa/opt/simplify_cfg.rs
index 46941775c5e..c282e2df451 100644
--- a/compiler/noirc_evaluator/src/ssa/opt/simplify_cfg.rs
+++ b/compiler/noirc_evaluator/src/ssa/opt/simplify_cfg.rs
@@ -18,7 +18,8 @@ use crate::ssa::{
         basic_block::BasicBlockId,
         cfg::ControlFlowGraph,
         function::{Function, RuntimeType},
-        instruction::TerminatorInstruction,
+        instruction::{Instruction, TerminatorInstruction},
+        value::Value,
     },
     ssa_gen::Ssa,
 };
@@ -31,6 +32,7 @@ impl Ssa {
     /// 4. Removing any blocks which have no instructions other than a single terminating jmp.
     /// 5. Replacing any jmpifs with constant conditions with jmps. If this causes the block to have
     ///    only 1 successor then (2) also will be applied.
+    /// 6. Replacing any jmpifs with a negated condition with a jmpif with a un-negated condition and reversed branches.
     ///
     /// Currently, 1 is unimplemented.
     #[tracing::instrument(level = "trace", skip(self))]
@@ -55,6 +57,8 @@ impl Function {
                 stack.extend(self.dfg[block].successors().filter(|block| !visited.contains(block)));
             }
 
+            check_for_negated_jmpif_condition(self, block, &mut cfg);
+
             // This call is before try_inline_into_predecessor so that if it succeeds in changing a
             // jmpif into a jmp, the block may then be inlined entirely into its predecessor in try_inline_into_predecessor.
             check_for_constant_jmpif(self, block, &mut cfg);
@@ -184,6 +188,55 @@ fn check_for_double_jmp(function: &mut Function, block: BasicBlockId, cfg: &mut
     cfg.recompute_block(function, block);
 }
 
+/// Optimize a jmpif on a negated condition by swapping the branches.
+fn check_for_negated_jmpif_condition(
+    function: &mut Function,
+    block: BasicBlockId,
+    cfg: &mut ControlFlowGraph,
+) {
+    if matches!(function.runtime(), RuntimeType::Acir(_)) {
+        // Swapping the `then` and `else` branches of a `JmpIf` within an ACIR function
+        // can result in the situation where the branches merge together again in the `then` block, e.g.
+        //
+        // acir(inline) fn main f0 {
+        //   b0(v0: u1):
+        //     jmpif v0 then: b2, else: b1
+        //   b2():
+        //     return
+        //   b1():
+        //     jmp b2()
+        // }
+        //
+        // This breaks the `flatten_cfg` pass as it assumes that merges only happen in
+        // the `else` block or a 3rd block.
+        //
+        // See: https://github.com/noir-lang/noir/pull/5891#issuecomment-2500219428
+        return;
+    }
+
+    if let Some(TerminatorInstruction::JmpIf {
+        condition,
+        then_destination,
+        else_destination,
+        call_stack,
+    }) = function.dfg[block].terminator()
+    {
+        if let Value::Instruction { instruction, .. } = function.dfg[*condition] {
+            if let Instruction::Not(negated_condition) = function.dfg[instruction] {
+                let call_stack = call_stack.clone();
+                let jmpif = TerminatorInstruction::JmpIf {
+                    condition: negated_condition,
+                    then_destination: *else_destination,
+                    else_destination: *then_destination,
+                    call_stack,
+                };
+                function.dfg[block].set_terminator(jmpif);
+                cfg.recompute_block(function, block);
+            }
+        }
+    }
+}
+
 /// If the given block has block parameters, replace them with the jump arguments from the predecessor.
 ///
 /// Currently, if this function is needed, `try_inline_into_predecessor` will also always apply,
@@ -246,6 +299,8 @@ mod test {
             map::Id,
             types::Type,
         },
+        opt::assert_normalized_ssa_equals,
+        Ssa,
     };
     use acvm::acir::AcirField;
 
@@ -359,4 +414,59 @@ mod test {
             other => panic!("Unexpected terminator {other:?}"),
         }
     }
+
+    #[test]
+    fn swap_negated_jmpif_branches_in_brillig() {
+        let src = "
+        brillig(inline) fn main f0 {
+          b0(v0: u1):
+            v1 = allocate -> &mut Field
+            store Field 0 at v1
+            v3 = not v0
+            jmpif v3 then: b1, else: b2
+          b1():
+            store Field 2 at v1
+            jmp b2()
+          b2():
+            v5 = load v1 -> Field
+            v6 = eq v5, Field 2
+            constrain v5 == Field 2
+            return
+        }";
+        let ssa = Ssa::from_str(src).unwrap();
+
+        let expected = "
+        brillig(inline) fn main f0 {
+          b0(v0: u1):
+            v1 = allocate -> &mut Field
+            store Field 0 at v1
+            v3 = not v0
+            jmpif v0 then: b2, else: b1
+          b2():
+            v5 = load v1 -> Field
+            v6 = eq v5, Field 2
+            constrain v5 == Field 2
+            return
+          b1():
+            store Field 2 at v1
+            jmp b2()
+        }";
+        assert_normalized_ssa_equals(ssa.simplify_cfg(), expected);
+    }
+
+    #[test]
+    fn does_not_swap_negated_jmpif_branches_in_acir() {
+        let src = "
+        acir(inline) fn main f0 {
+          b0(v0: u1):
+            v1 = not v0
+            jmpif v1 then: b1, else: b2
+          b1():
+            jmp b2()
+          b2():
+            return
+        }";
+        let ssa = Ssa::from_str(src).unwrap();
+        assert_normalized_ssa_equals(ssa.simplify_cfg(), src);
+    }
 }
diff --git a/test_programs/execution_success/negated_jmpif_condition/Nargo.toml b/test_programs/execution_success/negated_jmpif_condition/Nargo.toml
new file mode 100644
index 00000000000..c83e2c1c1fd
--- /dev/null
+++ b/test_programs/execution_success/negated_jmpif_condition/Nargo.toml
@@ -0,0 +1,6 @@
+[package]
+name = "negated_jmpif_condition"
+type = "bin"
+authors = [""]
+
+[dependencies]
diff --git a/test_programs/execution_success/negated_jmpif_condition/Prover.toml b/test_programs/execution_success/negated_jmpif_condition/Prover.toml
new file mode 100644
index 00000000000..151faa5a9b1
--- /dev/null
+++ b/test_programs/execution_success/negated_jmpif_condition/Prover.toml
@@ -0,0 +1 @@
+x = "2"
\ No newline at end of file
diff --git a/test_programs/execution_success/negated_jmpif_condition/src/main.nr b/test_programs/execution_success/negated_jmpif_condition/src/main.nr
new file mode 100644
index 00000000000..06de2b41820
--- /dev/null
+++ b/test_programs/execution_success/negated_jmpif_condition/src/main.nr
@@ -0,0 +1,9 @@
+fn main(mut x: Field) {
+    let mut q = 0;
+
+    if x != 10 {
+        q = 2;
+    }
+
+    assert(q == 2);
+}