SOP templatesPharmacy

Controlled Substances Handling SOP Template

A ready-to-use SOP for receiving, storing, dispensing and reconciling controlled substances, with two-person checks and daily balance verification to prevent diversion.

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Ilia PirozhenkoReviewed by Ilia Pirozhenko, Founder, Perfect WikiUpdated September 15, 202612 steps4 roles3 min read
Standard operating procedureSOP-PHA-002 ยท Rev 1.0
Owner
Pharmacist in Charge
Effective date
September 15, 2026
Review cycle
Every 6 months

1.Purpose

To handle controlled substances so that receipt, storage, dispensing and destruction are documented, balances are reconciled, and any loss or discrepancy is caught and reported quickly.

2.Scope

Applies to all scheduled controlled substances received, stored, dispensed and returned by the pharmacy. Follow your local law and the pharmacist in charge's policy for exact recordkeeping requirements.

Definitions

Perpetual inventory
A running, transaction-by-transaction balance of a controlled substance maintained alongside the physical stock.
Two-person verification
A check where a second authorized staff member independently confirms a count or transaction before it is finalized.
Diversion
The unauthorized removal or misuse of a controlled substance from legitimate pharmacy channels.

3.Responsibilities

Pharmacist
Performs final checks on controlled substance dispensing and daily balance reconciliation.
Pharmacy Technician
Assists with receiving counts, shelving and pulling stock under pharmacist oversight.
Pharmacist in Charge
Approves vault access, investigates discrepancies and reports losses as required by law.
Delivery Driver
Delivers wholesaler shipments and obtains signature confirmation for controlled substance deliveries.

RACI matrix

ActivityPharmacistPharmacy TechnicianPharmacist in ChargeDelivery Driver
Receive and count controlled substance shipmentARIC
Dispense a controlled substance prescriptionR/ACI-
Reconcile daily perpetual inventoryR/ACI-
Investigate and report a discrepancyRIA-
Approve vault or safe accessCIA-

R = Responsible, A = Accountable, C = Consulted, I = Informed

4.Materials and PPE

Materials, tools and systems

  • โ†’Locked vault or safe rated for controlled substance storage
  • โ†’Perpetual inventory log or software module
  • โ†’Official controlled substance order forms
  • โ†’Two-person count verification sheet
  • โ†’Discrepancy and loss report forms

Personal protective equipment

  • โ†’Disposable nitrile gloves

5.Procedure

  1. 5.1

    Verify the shipment against the order

    Pharmacist

    On delivery, compare the wholesaler's shipment to the original order form and packing slip, checking drug names, strengths and quantities before signing for receipt.

  2. 5.2

    Perform a two-person receiving count

    Pharmacy Technician

    Count each controlled substance item with a second authorized staff member present, and have both people sign the receiving count verification sheet.

    Checkpoint: The receiving count is signed by two authorized staff members before stock is shelved.

  3. 5.3

    Log the shipment into the perpetual inventory

    Pharmacist

    Enter the received quantity into the perpetual inventory log or software immediately after the count, updating the running balance for each item.

  4. 5.4

    Store in the vault or safe

    Pharmacy Technician

    Place controlled substances in the locked vault or safe designated for that schedule, restricting the combination or key to authorized staff only.

  5. 5.5

    Verify the prescription before dispensing

    Pharmacist

    Check the prescription for validity, prescriber authority and any red flags for diversion, such as early refill requests or unusual quantities, before filling.

    Warning: Do not dispense a controlled substance prescription that raises unresolved diversion concerns without further verification.

  6. 5.6

    Dispense with technician assistance

    Pharmacy Technician

    Have the technician pull and count the medication under direct pharmacist oversight, then hand off for the pharmacist's final check.

  7. 5.7

    Record the dispensing transaction

    Pharmacist

    Log the dispensed quantity in the perpetual inventory immediately, updating the running balance for that item and patient.

  8. 5.8

    Reconcile the daily balance

    Pharmacist

    At the end of each day, compare the physical count in the vault or safe against the perpetual inventory balance for each controlled substance.

    Checkpoint: The physical count matches the perpetual inventory balance before the reconciliation is signed off.

  9. 5.9

    Investigate any discrepancy immediately

    Pharmacist

    If the physical count does not match the perpetual inventory, recount immediately, review recent transactions, and document the investigation the same day.

  10. 5.10

    Report loss or theft

    Pharmacist in Charge

    Report any confirmed loss, theft or unresolved discrepancy to the pharmacist in charge and to the appropriate authorities as required by local law.

  11. 5.11

    Return expired or unused stock

    Pharmacist

    Segregate expired or unused controlled substances for return through an authorized reverse distributor, following the expired medication disposal SOP for documentation.

  12. 5.12

    Review vault access periodically

    Pharmacist in Charge

    Review the list of staff with vault or safe access on a set schedule, removing access for anyone who has changed roles or left the pharmacy.

6.Quality checks

  • โ†’Every receipt is counted and signed by two authorized staff.
  • โ†’The perpetual inventory balance matches the physical count at each daily reconciliation.
  • โ†’Every dispensing transaction is logged the same day it occurs.
  • โ†’Vault access is limited to staff on the current authorized list.

7.Records

  • โ†’Perpetual inventory log
  • โ†’Two-person receiving count sheets
  • โ†’Daily reconciliation records
  • โ†’Discrepancy and loss reports

8.KPIs

  • โ†’Number of unresolved discrepancies per month
  • โ†’Percentage of daily reconciliations completed on time
  • โ†’Average time to resolve a flagged discrepancy
  • โ†’Number of vault access changes reviewed per quarter

9.Common mistakes

  • โ†’Shelving a controlled substance delivery before completing the two-person count.
  • โ†’Delaying the perpetual inventory entry until later in the shift.
  • โ†’Skipping the daily reconciliation on a busy day.
  • โ†’Leaving vault access unreviewed after staff turnover.

10.Revision history

RevisionDateDescriptionReviewed by
1.0September 15, 2026Initial releaseIlia Pirozhenko

This is a template. Adapt it to your organization, equipment and local regulations before use.

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My daily count for a controlled substance is short by two tablets, what do I do?

Recount immediately and review the day's transactions in the perpetual inventory for a data entry error. If the discrepancy remains, document it the same day and report it to the pharmacist in charge without delay.Source: step 5.9 ยท Investigate any discrepancy immediately
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