diff --git a/jwst/extract_1d/soss_extract/soss_extract.py b/jwst/extract_1d/soss_extract/soss_extract.py
index 1a23994197..958322f3a0 100644
--- a/jwst/extract_1d/soss_extract/soss_extract.py
+++ b/jwst/extract_1d/soss_extract/soss_extract.py
@@ -1202,6 +1202,8 @@ def run_extract1d(input_model, spectrace_ref_name, wavemap_ref_name,
         # Pre-compute the weights for box extraction (used in modeling and extraction)
         args = (ref_files, transform, subarray, scidata_bkg.shape)
         box_weights, wavelengths = compute_box_weights(*args, width=soss_kwargs['width'])
+        if subarray == 'SUBSTRIP96':
+            box_weights['Order 2'] = np.ones((96, 2048))
 
         # Model the traces based on optics filter configuration (CLEAR or F277W)
         if soss_filter == 'CLEAR' and generate_model: