Bottomline Technologies Reconciliation to Non GAAP Measures Three Months Ended June 30, 2013

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Reconciliation to Measures Three Months Ended June 30, 2013 Non Cash Amortization of Equity Based Integration Restructuring Interest GAAP Intangible Assets Compensation Related Expenses Expenses Expense Subscriptions and transactions $ 30,359 $ $ $ $ $ $ 30,359 47% Software licenses 5,330 5,330 8% Service and maintenance 27,390 27,390 42% Equipment and supplies 1,953 1,953 3% Total revenues 65,032 65,032 100% Subscriptions and transactions 17,026 (188) (1,924) 14,914 51% Software licenses 421 421 92% Service and maintenance 11,436 (534) (12) 7 10,897 60% Equipment and supplies 1,553 1,553 20% Total cost of revenues 30,436 (722) (1,936) 7 27,785 Gross profit (loss) 34,596 722 1,936 (7) 37,247 57% Sales and marketing 16,182 (2,145) (91) 13,946 21% Product development 7,788 (431) (40) 3 7,320 11% General and administrative 7,494 (1,201) (1,315) 3 4,981 8% Amortization of intangible assets 4,874 (4,874) 0% Total operating expenses 36,338 (4,874) (3,777) (1,446) 6 26,247 40% Income (loss) from operations (1,742) 4,874 4,499 3,382 (13) 11,000 17% Other income (loss), net (3,249) 2,738 (511) 1% Income (loss) before income taxes (4,991) 4,874 4,499 3,382 (13) 2,738 10,489 16% Benefit for income taxes (1,177) (1,177) 2% Net Income (loss) (3,814) 4,874 4,499 3,382 (13) 2,738 11,666 18% Basic net loss per share $ (0.11) $ 0.08 Diluted net income (loss) per share $ (0.11) $ 0.08 $ 0.32 Basic 35,941 32,539 Diluted 35,941 34,433 36,694

Reconciliation to Measures Three Months Ended June 30, 2012 Amortization of Equity Based Integration Restructuring GAAP Intangible Assets Compensation Related Expenses Expenses Subscriptions and transactions $ 27,983 $ $ $ $ $ 27,983 46% Software licenses 4,969 4,969 8% Service and maintenance 26,440 26,440 43% Equipment and supplies 2,006 2,006 3% Total revenues 61,398 61,398 100% Subscriptions and transactions 12,690 (119) (70) (170) 12,331 56% Software licenses 462 462 91% Service and maintenance 12,896 (521) (28) (244) 12,103 54% Equipment and supplies 1,630 1,630 19% Total cost of revenues 27,678 (640) (98) (414) 26,526 Gross profit 33,720 640 98 414 34,872 57% Sales and marketing 14,399 (1,679) (129) (211) 12,380 20% Product development 9,327 (358) (70) (371) 8,528 14% General and administrative 5,990 (834) (683) (53) 4,420 7% Amortization of intangible assets 4,702 (4,702) 0% Total operating expenses 34,418 (4,702) (2,871) (882) (635) 25,328 41% Income (loss) from operations (698) 4,702 3,511 980 1,049 9,544 16% Other income, net 7 7 0% Income (loss) before income taxes (691) 4,702 3,511 980 1,049 9,551 16% Provision for income taxes 477 477 1% Net Income (loss) (1,168) 4,702 3,511 980 1,049 9,074 15% Basic net loss per share $ (0.03) Diluted net income (loss) per share $ (0.03) $ 0.26 Basic 34,744 Diluted 34,744 35,438

Reconciliation to Measures Fiscal Year Ended June 30, 2013 Net Loss Non Cash Amortization of Equity Based Integration Restructuring on Derivative Interest GAAP Intangible Assets Compensation Related Expenses Expenses Instruments Expense Subscriptions and transactions $ 118,016 $ $ $ $ $ $ $ 118,016 46% Software licenses 22,546 22,546 9% Service and maintenance 106,389 106,389 42% Equipment and supplies 7,823 7,823 3% Total revenues 254,774 254,774 100% Subscriptions and transactions 64,101 (921) (6,355) (174) 56,651 52% Software licenses 2,399 2,399 89% Service and maintenance 46,788 (2,423) (122) (141) 44,102 59% Equipment and supplies 5,998 5,998 23% Total cost of revenues 119,286 (3,344) (6,477) (315) 109,150 Gross profit 135,488 3,344 6,477 315 145,624 57% Sales and marketing 62,825 (8,370) (516) (295) 53,644 21% Product development 32,974 (1,808) (128) (86) 30,952 12% General and administrative 27,076 (4,509) (3,706) (483) 18,378 7% Amortization of intangible assets 19,549 (19,549) 0% Total operating expenses 142,424 (19,549) (14,687) (4,350) (864) 102,974 40% Income (loss) from operations (6,936) 19,549 18,031 10,827 1,179 42,650 17% Other income (loss), net (11,357) 4,435 5,980 (942) 0% Income (loss) before income taxes (18,293) 19,549 18,031 10,827 1,179 4,435 5,980 41,708 16% Benefit for income taxes (3,898) (3,898) 2% Net Income (loss) (14,395) 19,549 18,031 10,827 1,179 4,435 5,980 45,606 18% Basic net loss per share $ (0.41) Diluted net income (loss) per share $ (0.41) $ 1.26 Basic 35,444 Diluted 35,444 36,235

Reconciliation to Measures Fiscal Year Ended June 30, 2012 Amortization of Equity Based Integration Restructuring GAAP Intangible Assets Compensation Related Expenses Expenses Subscriptions and transactions $ 85,005 $ $ $ $ $ 85,005 38% Software licenses 17,562 17,562 8% Service and maintenance 113,832 113,832 50% Equipment and supplies 7,885 7,885 4% Total revenues 224,284 224,284 100% Subscriptions and transactions 41,266 (701) (102) (320) 40,143 53% Software licenses 2,082 2,082 88% Service and maintenance 51,559 (2,032) (41) (366) 49,120 57% Equipment and supplies 6,280 6,280 20% Total cost of revenues 101,187 (2,733) (143) (686) 97,625 Gross profit 123,097 2,733 143 686 126,659 56% Sales and marketing 49,902 (6,083) (286) (338) 43,195 19% Product development 28,687 (1,406) (89) (451) 26,741 12% General and administrative 21,495 (3,546) (1,469) (134) 16,346 7% Amortization of intangible assets 15,753 (15,753) 0% Total operating expenses 115,837 (15,753) (11,035) (1,844) (923) 86,282 38% Income from operations 7,260 15,753 13,768 1,987 1,609 40,377 18% Other income, net 41 41 0% Income before income taxes 7,301 15,753 13,768 1,987 1,609 40,418 18% Provision for income taxes 5,596 5,596 2% Net Income 1,705 15,753 13,768 1,987 1,609 34,822 16% Basic net income per share $ 0.05 Diluted net income per share $ 0.05 $ 0.99 Shares used in computing net income per share: Basic 34,268 Diluted 35,244 35,244

Reconciliation to Adjusted EBITDA Three months Ended Fiscal Year Ended 6/30/2013 6/30/2012 6/30/2013 6/30/2012 GAAP Net income (loss) $ (3,814) $ (1,168) $ (14,395) $ 1,705 Adjustments: Interest, other 3,249 (7) 11,357 (41) Taxes (1,177) 477 (3,898) 5,596 Depreciation 1,668 1,510 6,861 5,724 Amortization of intangible assets 4,874 4,702 19,549 15,753 Equity based compensation 4,499 3,511 18,031 13,768 integration related expenses 3,382 980 10,827 1,987 Restructuring expenses (benefit) (13) 1,049 1,179 1,609 Adjusted EBITDA 12,668 11,054 49,511 46,101